Select records that do not have associations outside a certain list
Here is the query

SELECT C.* FROM
(SELECT nid,COUNT(1) fullcount 
  FROM node 
  INNER JOIN field_data_dir_phys_category   AS category   ON node.nid = category.entity_id
  GROUP BY nid) A INNER JOIN
(SELECT nid,COUNT(1) goodcount 
  FROM node
  INNER JOIN field_data_dir_phys_category   AS category   ON node.nid = category.entity_id
  WHERE dir_phys_category_tid IN (498,499) GROUP BY nid) B USING (nid)
INNER JOIN (SELECT DISTINCT nid,title FROM node) C USING (nid)
WHERE fullcount=goodcount;


First, let's make some sample data. 
NOTE: this uses a single table.  The OP used two tables - mine is intended to demonstrate the method used to count categories, which is the central part of my answer.

DROP DATABASE IF EXISTS doub1ejack;
CREATE DATABASE doub1ejack;
USE doub1ejack
CREATE TABLE node
(
    id INT NOT NULL AUTO_INCREMENT,
    nid INT NOT NULL,
    title VARCHAR(20),
    dir_phys_category_tid INT NOT NULL,
    PRIMARY KEY (id)
);
INSERT INTO node (nid,title,dir_phys_category_tid) VALUES
(1171,'Toby',499),(1172,'Susan',500),(1172,'Susan',499),
(1172,'Susan',498),(1173,'Joseph',499),(1173,'Joseph',498);
SELECT * FROM node;


Let's load it

mysql&gt; DROP DATABASE IF EXISTS doub1ejack;
Query OK, 1 row affected (0.01 sec)

mysql&gt; CREATE DATABASE doub1ejack;
Query OK, 1 row affected (0.00 sec)

mysql&gt; USE doub1ejack
Database changed
mysql&gt; CREATE TABLE node
    -&gt; (
    -&gt;     id INT NOT NULL AUTO_INCREMENT,
    -&gt;     nid INT NOT NULL,
    -&gt;     title VARCHAR(20),
    -&gt;     dir_phys_category_tid INT NOT NULL,
    -&gt;     PRIMARY KEY (id)
    -&gt; );
Query OK, 0 rows affected (0.23 sec)

mysql&gt; INSERT INTO node (nid,title,dir_phys_category_tid) VALUES
    -&gt; (1171,'Toby',499),(1172,'Susan',500),(1172,'Susan',499),
    -&gt; (1172,'Susan',498),(1173,'Joseph',499),(1173,'Joseph',498);
Query OK, 6 rows affected (0.00 sec)
Records: 6  Duplicates: 0  Warnings: 0

mysql&gt;


Let's look at it

mysql&gt; SELECT * FROM node;
+----+------+--------+-----------------------+
| id | nid  | title  | dir_phys_category_tid |
+----+------+--------+-----------------------+
|  1 | 1171 | Toby   |                   499 |
|  2 | 1172 | Susan  |                   500 |
|  3 | 1172 | Susan  |                   499 |
|  4 | 1172 | Susan  |                   498 |
|  5 | 1173 | Joseph |                   499 |
|  6 | 1173 | Joseph |                   498 |
+----+------+--------+-----------------------+
6 rows in set (0.00 sec)

mysql&gt;


Next, let's run the proposed query

mysql&gt; SELECT C.* FROM
    -&gt; (SELECT nid,COUNT(1) fullcount FROM node GROUP BY nid) A
    -&gt; INNER JOIN
    -&gt; (SELECT nid,COUNT(1) goodcount FROM node
    -&gt; WHERE dir_phys_category_tid IN (498,499)
    -&gt; GROUP BY nid) B USING (nid)
    -&gt; INNER JOIN
    -&gt; (SELECT DISTINCT nid,title FROM node) C USING (nid)
    -&gt; WHERE fullcount=goodcount;
+------+--------+
| nid  | title  |
+------+--------+
| 1171 | Toby   |
| 1173 | Joseph |
+------+--------+
2 rows in set (0.00 sec)

mysql&gt;


OK why does it work ? Let's add the count columns, remove the WHERE and see

mysql&gt; SELECT C.*,fullcount,goodcount FROM
    -&gt; (SELECT nid,COUNT(1) fullcount FROM node GROUP BY nid) A
    -&gt; INNER JOIN
    -&gt; (SELECT nid,COUNT(1) goodcount FROM node
    -&gt; WHERE dir_phys_category_tid IN (498,499)
    -&gt; GROUP BY nid) B USING (nid)
    -&gt; INNER JOIN
    -&gt; (SELECT DISTINCT nid,title FROM node) C USING (nid)
    -&gt; ;
+------+--------+-----------+-----------+
| nid  | title  | fullcount | goodcount |
+------+--------+-----------+-----------+
| 1171 | Toby   |         1 |         1 |
| 1172 | Susan  |         3 |         2 |
| 1173 | Joseph |         2 |         2 |
+------+--------+-----------+-----------+
3 rows in set (0.00 sec)

mysql&gt;


Here is the correlation: When the number of categories (fullcount) is equal to the number of categories which are 498 and/or 499 (goodcount), then that row's nid is acceptable.

Give it a Try !!!