I get the impression that the only armor set bonuses in the game are those for level 50 characters (Columi gear, Rakata gear, etc.) At least, those are the only armor set bonuses I can find any information on.
Is this correct, or are my characters losing out for wearing mismatched gear?
Only the Tionese, Columi, and Rakata gear at level 60 ahs set bonuses. So, you're OK!