When you look at your messages window you'll notice the message "Warning: Null value is eliminated by an aggregate or other SET operation." which will explain your situation.

It is because you are counting the item in the column containing the NULL values. These NULL values will (default) be eliminated in the count. To get the desired results you can count on another column or all columns. See the example below:

create table #test (id int, value int)

insert into #test

select 1,1

union all select 2,null

union all select 3,null

union all select 4,2

select

count(value) as total_NULL_column

, count(ID) as total_ID_column

, count(*) as total_all_columns

from #test

where value is null

drop table #test