sql_slovak_cp1250_ci_as vs Slovak_CI_AS
Collation determines two things. 


The code page used (and hence characters that can be stored) for non unicode data.
The comparison semantics for all textual data.


(NB: SQL Server 2012 also introduces _SC, supplementary character, collations for  UTF-16 encoding rather than UCS-2 but these are not relevant to your question here)



SELECT *
FROM   sys.fn_helpcollations()
WHERE  name LIKE '%Slovak%CI%AS'


Returns the following information

name                      description
------------------------- -------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Slovak_CI_AS              Slovak, case-insensitive, accent-sensitive, kanatype-insensitive, width-insensitive
Slovak_100_CI_AS          Slovak-100, case-insensitive, accent-sensitive, kanatype-insensitive, width-insensitive
SQL_Slovak_CP1250_CI_AS   Slovak, case-insensitive, accent-sensitive, kanatype-insensitive, width-insensitive for Unicode Data, SQL Server Sort Order 94 on Code Page 1250 for non-Unicode Data


So on 2012 there are two windows collations and one SQL Collation. The description doesn't indicate the code page for the windows versions but that they are all the same can be seen from below.

CREATE TABLE #Collations
(
     code TINYINT PRIMARY KEY,
     SQL_Slovak_CP1250_CI_AS CHAR(1) COLLATE SQL_Slovak_CP1250_CI_AS,
     Slovak_CI_AS CHAR(1) COLLATE Slovak_CI_AS,
     Slovak_100_CI_AS CHAR(1) COLLATE Slovak_100_CI_AS,
     /*Included just to show an example of a different code page*/
     Latin1_General_CI_AS CHAR(1) COLLATE Latin1_General_CI_AS
);

WITH E00(N) AS (SELECT 1 UNION ALL SELECT 1),   --2
        E02(N) AS (SELECT 1 FROM E00 a, E00 b), --4
        E04(N) AS (SELECT 1 FROM E02 a, E02 b), --16
        E08(N) AS (SELECT 1 FROM E04 a, E04 b) --256
INSERT INTO #Collations
            (code)
SELECT ROW_NUMBER() OVER (ORDER BY (SELECT 0)) - 1
FROM   E08

UPDATE #Collations
SET    SQL_Slovak_CP1250_CI_AS = CAST(code AS BINARY(1)),
       Slovak_CI_AS = CAST(code AS BINARY(1)),
       Slovak_100_CI_AS = CAST(code AS BINARY(1)),
       Latin1_General_CI_AS = CAST(code AS BINARY(1))

SELECT *
FROM   #Collations 


Or, alternatively, using the COLLATIONPROPERTY function

SELECT COLLATIONPROPERTY('SQL_Slovak_CP1250_CI_AS', 'CodePage') AS SQL_Slovak_CP1250_CI_AS,
       COLLATIONPROPERTY('Slovak_CI_AS', 'CodePage')            AS Slovak_CI_AS,
       COLLATIONPROPERTY('Slovak_100_CI_AS', 'CodePage')        AS Slovak_100_CI_AS,
       COLLATIONPROPERTY('Latin1_General_CI_AS', 'CodePage')    AS Latin1_General_CI_AS


Returns

+-------------------------+--------------+------------------+----------------------+
| SQL_Slovak_CP1250_CI_AS | Slovak_CI_AS | Slovak_100_CI_AS | Latin1_General_CI_AS |
+-------------------------+--------------+------------------+----------------------+
|                    1250 |         1250 |             1250 |                 1252 |
+-------------------------+--------------+------------------+----------------------+ 


So as far as point 1 is concerned the collation makes no difference for SQL_Slovak_CP1250_CI_AS vs Slovak_CI_AS. 

For point 2 see Comparing SQL collations to Windows collations. The Collation semantics section has some discussion about how the two differ but skipping ahead to Recommendations


  SQL collations are provided for backward compatibility with earlier
  versions of SQL Server. Windows collations provide consistent string
  comparisons for both Unicode and for non-Unicode text in SQL Server
  that are also consistent with string comparisons in the Windows
  operating system. For all these reasons, Windows collations are
  preferred unless there are backward compatibility issues or specific
  performance issues that require a SQL collation.


So you should be using the Windows Collations anyway unless you have some specific backward compatibility need. Also I would use Slovak_100_CI_AS as this is more recent and avoids issues like this.

To see examples of specifics of how the comparison semantics differ between the three collations you can use the temporary table created earlier and try 

SELECT code,
       /*Exclude some characters that will mess up the formatting*/
       CASE WHEN code IN (9,10,12,13) THEN '' ELSE SQL_Slovak_CP1250_CI_AS END AS [Char], 
       DENSE_RANK() OVER (ORDER BY SQL_Slovak_CP1250_CI_AS) AS SQL_Slovak_CP1250_CI_AS,
       DENSE_RANK() OVER (ORDER BY Slovak_CI_AS) AS Slovak_CI_AS,       
       DENSE_RANK() OVER (ORDER BY Slovak_100_CI_AS) AS Slovak_100_CI_AS
FROM   #Collations 
ORDER BY SQL_Slovak_CP1250_CI_AS


That yields the following results

+------+------+-------------------------+--------------+------------------+
| code | Char | SQL_Slovak_CP1250_CI_AS | Slovak_CI_AS | Slovak_100_CI_AS |
+------+------+-------------------------+--------------+------------------+
|    0 |      |                       1 |            1 |                1 |
|    1 |      |                       2 |            2 |                2 |
|    2 |      |                       3 |            3 |                3 |
|    3 |      |                       4 |            4 |                4 |
|    4 |      |                       5 |            5 |                5 |
|    5 |      |                       6 |            6 |                6 |
|    6 |      |                       7 |            7 |                7 |
|    7 |      |                       8 |            8 |                8 |
|    8 |      |                       9 |            9 |                9 |
|   14 |      |                      10 |           10 |               10 |
|   15 |      |                      11 |           11 |               11 |
|   16 |      |                      12 |           12 |               12 |
|   17 |      |                      13 |           13 |               13 |
|   18 |      |                      14 |           14 |               14 |
|   19 |      |                      15 |           15 |               15 |
|   20 |      |                      16 |           16 |               16 |
|   21 |      |                      17 |           17 |               17 |
|   22 |      |                      18 |           18 |               18 |
|   23 |      |                      19 |           19 |               19 |
|   24 |      |                      20 |           20 |               20 |
|   25 |      |                      21 |           21 |               21 |
|   26 |      |                      22 |           22 |               22 |
|   27 |      |                      23 |           23 |               23 |
|   28 |      |                      24 |           24 |               24 |
|   29 |      |                      25 |           25 |               25 |
|   30 |      |                      26 |           26 |               26 |
|   31 |      |                      27 |           27 |               27 |
|  127 |      |                      28 |           28 |               28 |
|  129 |      |                      29 |           29 |              106 |
|  131 |      |                      30 |           30 |              107 |
|  136 |      |                      31 |           31 |              108 |
|  144 |      |                      32 |           32 |              109 |
|  152 |      |                      33 |           33 |              110 |
|   39 | '    |                      34 |           34 |               29 |
|   45 | -    |                      35 |           35 |               30 |
|  173 | ­     |                      36 |           36 |                1 |
|  150 | –    |                      37 |           37 |               31 |
|  151 | —    |                      38 |           38 |               32 |
|   32 |      |                      39 |            1 |                1 |
|  160 |      |                      40 |           39 |               33 |
|    9 |      |                      41 |           40 |               34 |
|   10 |      |                      42 |           41 |               35 |
|   11 |      |                      43 |           42 |               36 |
|   12 |      |                      44 |           43 |               37 |
|   13 |      |                      45 |           44 |               38 |
|   33 | !    |                      46 |           45 |               39 |
|   34 | "    |                      47 |           46 |               40 |
|   35 | #    |                      48 |           47 |               41 |
|   36 | $    |                      49 |           48 |               42 |
|   37 | %    |                      50 |           49 |               43 |
|   38 | &amp;    |                      51 |           50 |               44 |
|   40 | (    |                      52 |           51 |               45 |
|   41 | )    |                      53 |           52 |               46 |
|   42 | *    |                      54 |           53 |               47 |
|   44 | ,    |                      55 |           54 |               48 |
|   46 | .    |                      56 |           55 |               49 |
|   47 | /    |                      57 |           56 |               50 |
|   58 | :    |                      58 |           57 |               51 |
|   59 | ;    |                      59 |           58 |               52 |
|   63 | ?    |                      60 |           59 |               53 |
|   64 | @    |                      61 |           60 |               54 |
|   91 | [    |                      62 |           61 |               55 |
|   92 | \    |                      63 |           62 |               56 |
|   93 | ]    |                      64 |           63 |               57 |
|   94 | ^    |                      65 |           64 |               58 |
|   95 | _    |                      66 |           65 |               59 |
|   96 | `    |                      67 |           66 |               60 |
|  123 | {    |                      68 |           67 |               61 |
|  124 | |    |                      69 |           68 |               62 |
|  125 | }    |                      70 |           69 |               63 |
|  126 | ~    |                      71 |           70 |               64 |
|  166 | ¦    |                      72 |           71 |               65 |
|  168 | ¨    |                      73 |           72 |               66 |
|  180 | ´    |                      74 |           73 |               67 |
|  184 | ¸    |                      75 |           74 |               68 |
|  161 | ˇ    |                      76 |           75 |               69 |
|  162 | ˘    |                      77 |           76 |               70 |
|  255 | ˙    |                      78 |           77 |               71 |
|  178 | ˛    |                      79 |           78 |               72 |
|  189 | ˝    |                      80 |           79 |               73 |
|  145 | ‘    |                      81 |           80 |               74 |
|  146 | ’    |                      82 |           81 |               75 |
|  130 | ‚    |                      83 |           82 |               76 |
|  147 | “    |                      84 |           83 |               77 |
|  148 | ”    |                      85 |           84 |               78 |
|  132 | „    |                      86 |           85 |               79 |
|  139 | ‹    |                      87 |           86 |               80 |
|  155 | ›    |                      88 |           87 |               81 |
|   43 | +    |                      89 |           88 |               84 |
|   60 | &lt;    |                      90 |           89 |               85 |
|   61 | =    |                      91 |           90 |               86 |
|   62 | &gt;    |                      92 |           91 |               87 |
|  177 | ±    |                      93 |           92 |               88 |
|  171 | «    |                      94 |           93 |               89 |
|  187 | »    |                      95 |           94 |               90 |
|  215 | ×    |                      96 |           95 |               91 |
|  247 | ÷    |                      97 |           96 |               92 |
|  164 | ¤    |                      98 |           97 |               82 |
|  167 | §    |                      99 |           98 |               93 |
|  169 | ©    |                     100 |           99 |               94 |
|  172 | ¬    |                     101 |          100 |               95 |
|  174 | ®    |                     102 |          101 |               96 |
|  176 | °    |                     103 |          102 |               97 |
|  181 | µ    |                     104 |          103 |               98 |
|  182 | ¶    |                     105 |          104 |               99 |
|  183 | ·    |                     106 |          105 |              100 |
|  134 | †    |                     107 |          106 |              102 |
|  135 | ‡    |                     108 |          107 |              103 |
|  149 | •    |                     109 |          108 |              104 |
|  133 | …    |                     110 |          109 |              101 |
|  137 | ‰    |                     111 |          110 |              105 |
|  128 | €    |                     112 |          111 |               83 |
|   48 | 0    |                     113 |          112 |              111 |
|   49 | 1    |                     114 |          113 |              112 |
|   50 | 2    |                     115 |          114 |              113 |
|   51 | 3    |                     116 |          115 |              114 |
|   52 | 4    |                     117 |          116 |              115 |
|   53 | 5    |                     118 |          117 |              116 |
|   54 | 6    |                     119 |          118 |              117 |
|   55 | 7    |                     120 |          119 |              118 |
|   56 | 8    |                     121 |          120 |              119 |
|   57 | 9    |                     122 |          121 |              120 |
|   97 | a    |                     123 |          122 |              121 |
|   65 | A    |                     123 |          122 |              121 |
|  193 | Á    |                     124 |          123 |              122 |
|  225 | á    |                     124 |          123 |              122 |
|  226 | â    |                     125 |          124 |              123 |
|  194 | Â    |                     125 |          124 |              123 |
|  195 | Ă    |                     126 |          125 |              124 |
|  227 | ă    |                     126 |          125 |              124 |
|  185 | ą    |                     127 |          126 |              125 |
|  165 | Ą    |                     127 |          126 |              125 |
|  196 | Ä    |                     128 |          127 |              126 |
|  228 | ä    |                     128 |          127 |              126 |
|   66 | B    |                     129 |          128 |              127 |
|   98 | b    |                     129 |          128 |              127 |
|   99 | c    |                     130 |          129 |              128 |
|   67 | C    |                     130 |          129 |              128 |
|  230 | ć    |                     131 |          130 |              129 |
|  198 | Ć    |                     131 |          130 |              129 |
|  199 | Ç    |                     132 |          131 |              130 |
|  231 | ç    |                     132 |          131 |              130 |
|  232 | č    |                     133 |          132 |              131 |
|  200 | Č    |                     133 |          132 |              131 |
|   68 | D    |                     134 |          133 |              132 |
|  100 | d    |                     134 |          133 |              132 |
|  239 | ď    |                     135 |          134 |              133 |
|  207 | Ď    |                     135 |          134 |              133 |
|  208 | Đ    |                     136 |          135 |              134 |
|  240 | đ    |                     136 |          135 |              134 |
|  101 | e    |                     137 |          136 |              135 |
|   69 | E    |                     137 |          136 |              135 |
|  235 | ë    |                     138 |          137 |              136 |
|  203 | Ë    |                     138 |          137 |              136 |
|  201 | É    |                     139 |          138 |              137 |
|  233 | é    |                     139 |          138 |              137 |
|  236 | ě    |                     140 |          139 |              138 |
|  204 | Ě    |                     140 |          139 |              138 |
|  202 | Ę    |                     141 |          140 |              139 |
|  234 | ę    |                     141 |          140 |              139 |
|   70 | F    |                     142 |          141 |              140 |
|  102 | f    |                     142 |          141 |              140 |
|  103 | g    |                     143 |          142 |              141 |
|   71 | G    |                     143 |          142 |              141 |
|   72 | H    |                     144 |          143 |              142 |
|  104 | h    |                     144 |          143 |              142 |
|  105 | i    |                     145 |          144 |              143 |
|   73 | I    |                     145 |          144 |              143 |
|  237 | í    |                     146 |          145 |              144 |
|  205 | Í    |                     146 |          145 |              144 |
|  206 | Î    |                     147 |          146 |              145 |
|  238 | î    |                     147 |          146 |              145 |
|   74 | J    |                     148 |          147 |              146 |
|  106 | j    |                     148 |          147 |              146 |
|  107 | k    |                     149 |          148 |              147 |
|   75 | K    |                     149 |          148 |              147 |
|   76 | L    |                     150 |          149 |              148 |
|  108 | l    |                     150 |          149 |              148 |
|  229 | ĺ    |                     151 |          150 |              149 |
|  197 | Ĺ    |                     151 |          150 |              149 |
|  188 | Ľ    |                     152 |          151 |              150 |
|  190 | ľ    |                     152 |          151 |              150 |
|  179 | ł    |                     153 |          152 |              151 |
|  163 | Ł    |                     153 |          152 |              151 |
|   77 | M    |                     154 |          153 |              152 |
|  109 | m    |                     154 |          153 |              152 |
|  110 | n    |                     155 |          154 |              153 |
|   78 | N    |                     155 |          154 |              153 |
|  209 | Ń    |                     156 |          155 |              154 |
|  241 | ń    |                     156 |          155 |              154 |
|  242 | ň    |                     157 |          156 |              155 |
|  210 | Ň    |                     157 |          156 |              155 |
|   79 | O    |                     158 |          157 |              156 |
|  111 | o    |                     158 |          157 |              156 |
|  214 | Ö    |                     159 |          158 |              157 |
|  246 | ö    |                     159 |          158 |              157 |
|  211 | Ó    |                     160 |          159 |              158 |
|  243 | ó    |                     160 |          159 |              158 |
|  213 | Ő    |                     161 |          160 |              159 |
|  245 | ő    |                     161 |          160 |              159 |
|  212 | Ô    |                     162 |          161 |              160 |
|  244 | ô    |                     162 |          161 |              160 |
|  112 | p    |                     163 |          162 |              161 |
|   80 | P    |                     163 |          162 |              161 |
|   81 | Q    |                     164 |          163 |              162 |
|  113 | q    |                     164 |          163 |              162 |
|  114 | r    |                     165 |          164 |              163 |
|   82 | R    |                     165 |          164 |              163 |
|  192 | Ŕ    |                     166 |          165 |              164 |
|  224 | ŕ    |                     166 |          165 |              164 |
|  248 | ř    |                     167 |          166 |              165 |
|  216 | Ř    |                     167 |          166 |              165 |
|   83 | S    |                     168 |          167 |              166 |
|  115 | s    |                     168 |          167 |              166 |
|  156 | ś    |                     169 |          168 |              167 |
|  140 | Ś    |                     169 |          168 |              167 |
|  170 | Ş    |                     170 |          169 |              168 |
|  186 | ş    |                     170 |          169 |              168 |
|  223 | ß    |                     171 |          170 |              169 |
|  138 | Š    |                     172 |          171 |              170 |
|  154 | š    |                     172 |          171 |              170 |
|   84 | T    |                     173 |          172 |              171 |
|  116 | t    |                     173 |          172 |              171 |
|  157 | ť    |                     174 |          173 |              172 |
|  141 | Ť    |                     174 |          173 |              172 |
|  254 | ţ    |                     175 |          174 |              173 |
|  222 | Ţ    |                     175 |          174 |              173 |
|  153 | ™    |                     176 |          175 |              174 |
|   85 | U    |                     177 |          176 |              175 |
|  117 | u    |                     177 |          176 |              175 |
|  220 | Ü    |                     178 |          177 |              176 |
|  252 | ü    |                     178 |          177 |              176 |
|  250 | ú    |                     179 |          178 |              177 |
|  218 | Ú    |                     179 |          178 |              177 |
|  217 | Ů    |                     180 |          179 |              178 |
|  249 | ů    |                     180 |          179 |              178 |
|  251 | ű    |                     181 |          180 |              179 |
|  219 | Ű    |                     181 |          180 |              179 |
|  118 | v    |                     182 |          181 |              180 |
|   86 | V    |                     182 |          181 |              180 |
|   87 | W    |                     183 |          182 |              181 |
|  119 | w    |                     183 |          182 |              181 |
|  120 | x    |                     184 |          183 |              182 |
|   88 | X    |                     184 |          183 |              182 |
|   89 | Y    |                     185 |          184 |              183 |
|  121 | y    |                     185 |          184 |              183 |
|  221 | Ý    |                     186 |          185 |              184 |
|  253 | ý    |                     186 |          185 |              184 |
|  122 | z    |                     187 |          186 |              185 |
|   90 | Z    |                     187 |          186 |              185 |
|  191 | ż    |                     188 |          187 |              186 |
|  175 | Ż    |                     188 |          187 |              186 |
|  159 | ź    |                     189 |          188 |              187 |
|  143 | Ź    |                     189 |          188 |              187 |
|  142 | Ž    |                     190 |          189 |              188 |
|  158 | ž    |                     190 |          189 |              188 |
+------+------+-------------------------+--------------+------------------+