Mints "Bunny" ears are missing...

Probably just removed them off to make room for the other pair. Three pairs of ears would be a bit much on her.

...you do know they can come off, right?

Crap, that first 'off' is a typo since I originally typed "took them off".

Oops.

I doubt it, Mint seems to be born with those ears, so maybe she covered them up with her second pair.

Um, no. She takes them off at least two times in the course of the anime. They aren't permanently attached.