I did thought about that extra bones are using now extra data. And unfortunately animation is one of the oldest part of engine that hasn’t been touched for long ago. I don’t really know how to dispose them, and not sure even you can.
So yes, there is some overhead of having that many models. But you probably need to test and see how it performs, it might be not a problem at all.
We are thinking a lot about new Animation system, that would be built from ground-up as new thing. It won’t be easy task, but we have loads of plans for it. But it won’t come any time soon.