Blizzard hasn't made it clear what they plan on doing with extra companions stored away on various toons/banks once MoP is released.
At the moment on the beta, any already known pets (the actual items, not a caged version) cannot be learned by a toon that already knows the spell for it. This might change and shouldn't be seen as how pets will work in the final version, though.
So for example, I have two extra Toxic Wastelings and two Clockwork Rocket Bots on my main. She already has both pets in her collection so she cannot add those extra pets to the Pet Journal. An "already known" error pops up when I try. If, however, those extra pets were on alts that didn't know them, I'd be able to add a second (and possibly third) to my collection.
You can learn a second/third caged version, though. It's kind of weird like that, but that's to be expected since it's still the beta and a work in progress.