well what i do is setup an external folder on my HD that isn't in adobe's default brushes folder.
What this does is speed up the loading of
PS because it doesn't have to load so many brushes.
and secondly if you choose the "load brushes" option, you can still locate and load brushes, manually, so you don't have all 50 sets loaded at a time, only the Default brushes and the Ones you needed for the project at hand.
As for your "subfolders" question, I have no idea, I never tried.