There's a rumor floating around that come MoP, if you have more than 3 of the same pet, those extras will automatically be removed.
According to a Tweet by game developer Mumper, THIS IS NOT THE CASE. Pets will not be removed and players will be able to retain duplicates for caging and trading.
However, if you have over 500 pets, you will still not be able to add any new pets to your journal. In order to learn a new one, you'll need to drop below the cap first. This hasn't and will not change.
Anyway, breathe easy collectors! You won't have to get rid of all your duplicates prior to MoP. So sit back, relax, plan for some reorganizing in MoP, but mainly enjoy your account-wide collection. Don't forget to start renaming those babies! :)