Você deve poder usar subconsultas para isso:
SELECT
(SELECT COUNT(*) FROM ... WHERE ...)
- (SELECT COUNT(*) FROM ... WHERE ...) AS Difference
Acabei de testar:
Difference
-----------
45
(1 row(s) affected)
SELECT
(SELECT COUNT(*) FROM ... WHERE ...)
- (SELECT COUNT(*) FROM ... WHERE ...) AS Difference
Difference
-----------
45
(1 row(s) affected)