Optimizing Slick generated SQL query
Since you have written you are using PostgreSQL, then I would not worry, since PostgreSQL is known for a really good query optimizer. Such a simple transformation is effortless, it takes virtually no additional time. The only thing is you wait, the problem is eventually going to be fixed upstream (somewhere around Slick version 3.1) and you don't have to do anything.
p.s.: Why are you not simply using this query? It should return exactly the same result, if you have a foreign constraint on the tables:
SELECT id, COUNT(*) FROM cart_product WHERE id=3