How to capture missing information in SQL Server tables
Retain the correct data types in each column.  Use what is referred to as a magic number to indicate "not applicable", or "unknown".

For instance, with an int column, you might use -2147483647 to indicate "not applicable", and -2147483646 to indicate "unknown", presuming those two values do not show up in the "normal" data.  For dates, use values like N'1900-01-01T00:00:00' and N'1900-01-01T00:00:01'.  Of course, you'll need to programmatically exclude these values when performing statistical analysis or reporting, since they would skew things like averages and sums.  

An example table containing an int column using magic numbers:

CREATE TABLE dbo.Items
(
    SomeValue int NOT NULL
    , CONSTRAINT CK_SomeValue
        CHECK (
            SomeValue = -2147483647 /* Not Applicable */
            OR SomeValue = -2147483646 /* Unknown */
            OR (SomeValue &gt; 0 AND SomeValue &lt; 2147483648)
            )
);


Note, the check constraint that "documents" the magic/canary values.  As Erik Darling details in a blog post, canary values remove the need for the column to allow NULLs, which in turn can alleviate some nasty surprises when using NOT IN (...) and JOIN ON ISNULL(...) = ISNULL(...), etc.

An example may be the best way to show the problems associated with using magic/canary values, and using NULL values instead.  We'll do this work in tempdb, and create two almost identical tables.  One uses magic/canary values, one uses NULL instead.

USE tempdb; 

IF OBJECT_ID(N'dbo.ItemsNoNulls', N'U') IS NOT NULL
DROP TABLE dbo.ItemsNoNulls;
IF OBJECT_ID(N'dbo.ItemsNulls', N'U') IS NOT NULL
DROP TABLE dbo.ItemsNulls;

CREATE TABLE dbo.ItemsNoNulls
(
    SomeValue int NOT NULL
    , CONSTRAINT CK_ItemsNoNulls_SomeValue
        CHECK (
            SomeValue = -2147483647 /* Unknown */
            OR SomeValue = -2147483646 /* Not Applicable */
            OR (SomeValue &gt; 0 AND SomeValue &lt; 2147483648)
            )
);

CREATE TABLE dbo.ItemsNulls
(
    SomeValue int NULL
    , CONSTRAINT CK_ItemsNulls_SomeValue
        CHECK (
            SomeValue IS NULL
            OR (SomeValue &gt; 0 AND SomeValue &lt; 2147483648)
            )
);


Here, we'll insert a load of rows where 2% of the rows are "magic" values of either -2147483647 or -2147483646:

;WITH src AS (
    SELECT val = ABS(CONVERT(int, CRYPT_GEN_RANDOM(4)))
    FROM sys.columns c1
        CROSS JOIN sys.columns c2
)
INSERT INTO dbo.ItemsNoNulls(SomeValue)
SELECT CASE src.val % 50 
    WHEN 1 THEN -2147483647
    WHEN 2 THEN -2147483646
    ELSE src.val
END
FROM src;


This will insert those previously generated rows into the table where NULL represents Unknown or Not Available:

INSERT INTO dbo.ItemsNulls (SomeValue)
SELECT CASE inn.SomeValue
        WHEN -2147483647 THEN NULL
        WHEN -2147483646 THEN NULL
        ELSE inn.SomeValue
    END
FROM dbo.ItemsNoNulls inn


Compare the output of these two simple queries:

SELECT [Avg] = AVG(CONVERT(bigint, SomeValue))
    , [Count] = COUNT(SomeValue)
FROM dbo.ItemsNoNulls;


╔═══════════╦════════╗
║ Avg       ║ Count  ║
╠═══════════╬════════╣
║ 944303347 ║ 549081 ║
╚═══════════╩════════╝


SELECT [Avg] = AVG(CONVERT(bigint, SomeValue))
    , [Count] = COUNT(SomeValue)
    , [CountNull] = COUNT(COALESCE(SomeValue, 0))
FROM dbo.ItemsNulls


╔════════════╦════════╦═══════════╗
║ Avg        ║ Count  ║ CountNull ║
╠════════════╬════════╬═══════════╣
║ 1073162998 ║ 527112 ║ 549081    ║
╚════════════╩════════╩═══════════╝


The "average" in the first resultset is artificially low because of the presence of the canary values.  The "count" in the second query is lower than expected since aggregates eliminate NULL values, as shown by the warning:


  Warning: Null value is eliminated by an aggregate or other SET operation.


If we modify the first query to eliminate the canary values:

SELECT [Avg] = AVG(CONVERT(bigint, SomeValue))
    , [Count] = COUNT(SomeValue)
FROM dbo.ItemsNoNulls
WHERE SomeValue &lt;&gt; -2147483647
    AND SomeValue &lt;&gt; -2147483646;


We get the correct average value, however the count no longer reflects the actual number of rows in the table:

╔════════════╦════════╗
║ Avg        ║ Count  ║
╠════════════╬════════╣
║ 1073162998 ║ 527112 ║
╚════════════╩════════╝


To get the accurate average, and an accurate count, we need to do something like:

SELECT [Avg] = AVG(CONVERT(bigint, SomeValue))
    , [Count] = (SELECT COUNT(SomeValue) FROM dbo.ItemsNoNulls)
FROM dbo.ItemsNoNulls
WHERE SomeValue &lt;&gt; -2147483647
    AND SomeValue &lt;&gt; -2147483646;


╔════════════╦════════╗
║ Avg        ║ Count  ║
╠════════════╬════════╣
║ 1073162998 ║ 549081 ║
╚════════════╩════════╝


As you can see, both NULL columns and magic/canary values introduce some unexpected problems that can be bad for reporting.  Making sure you and other team members fully understand the implications is extremely important for accuracy.

One other method of recording "unknown" or "not applicable" values is to allow NULL values on those columns, combined with a separate column that indicates the status of the value.  For example:

USE tempdb;
IF OBJECT_ID(N'dbo.Items', N'U') IS NOT NULL
DROP TABLE dbo.Items;
IF OBJECT_ID(N'dbo.StatusValues', N'U') IS NOT NULL
DROP TABLE dbo.StatusValues;

CREATE TABLE dbo.StatusValues
(
    StatusValue int NOT NULL
        CONSTRAINT PK_StatusValues
        PRIMARY KEY CLUSTERED
    , StatusDescription varchar(30) NOT NULL
);

INSERT INTO dbo.StatusValues (StatusValue, StatusDescription)
VALUES (0, 'Normal')
    , (1, 'Unknown')
    , (2, 'Not Applicable');

CREATE TABLE dbo.Items
(
    SomeValue int NULL
    , SomeValueStatus int NOT NULL
        CONSTRAINT FK_StatusValue
        FOREIGN KEY REFERENCES dbo.StatusValues(StatusValue)
    , CONSTRAINT CK_ValueStatus
        CHECK ((SomeValue IS NULL AND (SomeValueStatus = 1 OR SomeValueStatus = 2))
            OR (SomeValue IS NOT NULL AND (SomeValueStatus = 0)))
);


This series of statements shows how the check constraint prevents invalid inserts:

--this fails, since 0 indicates a status of "normal"
INSERT INTO dbo.Items (SomeValue, SomeValueStatus)
VALUES (NULL, 0);

--this succeeds since status "1" is Unknown
INSERT INTO dbo.Items (SomeValue, SomeValueStatus)
VALUES (NULL, 1);

--this succeeds since status "2" is Not Applicable
INSERT INTO dbo.Items (SomeValue, SomeValueStatus)
VALUES (NULL, 2);

--this succeeds since the SomeValue column contains a non-null value
INSERT INTO dbo.Items (SomeValue, SomeValueStatus)
VALUES (1, 0);

--this fails since "Unknown" is incompatible with a non-null SomeValue
INSERT INTO dbo.Items (SomeValue, SomeValueStatus)
VALUES (1, 1);

--this fails since "Not Applicable" is incompatible with a non-null SomeValue
INSERT INTO dbo.Items (SomeValue, SomeValueStatus)
VALUES (1, 2);


The contents of the table:

SELECT i.SomeValue
    , sv.StatusDescription
FROM dbo.Items i
    INNER JOIN dbo.StatusValues sv ON i.SomeValueStatus = sv.StatusValue; 


╔═══════════╦═══════════════════╗
║ SomeValue ║ StatusDescription ║
╠═══════════╬═══════════════════╣
║ NULL      ║ Unknown           ║
║ NULL      ║ Not Applicable    ║
║ 1         ║ Normal            ║
╚═══════════╩═══════════════════╝


The inserts above that are invalid will cause the following error to be returned to the client:


  Msg 547, Level 16, State 0, Line 30
  The INSERT statement conflicted with the CHECK constraint "CK_ValueStatus". The conflict occurred in database "tempdb", table "dbo.Items".