MySQL Wybierz z kategorii w tabeli y, gdzie Count (produkt kategorii z innej tabeli) jest większy od zera

Możesz użyć EXISTS :

SELECT category, categoryID 
FROM categories AS c
WHERE EXISTS (SELECT 1 
              FROM products AS p
              WHERE p.categoryID  = c.categoryID )

lub INNER JOIN :

SELECT DISTINCT category, categoryID 
FROM categories AS c
INNER JOIN products AS p ON p.categoryID  = c.categoryID

lub IN operator:

SELECT category, categoryID 
FROM categories 
WHERE categoryID IN (SELECT categoryID FROM products)