It's definitely possible to do hundreds of skins for this sort of thing. We're doing that on our project (four spritesheets and counting so far) and it still performs well. Organization is the real problem. Use a good naming system and file structure.
I have been thinking for a while about cutting some parts out into a separate skeleton, though. For some FX related things. Just haven't put in the time to figure it out yet. Maybe with the SkeletonRenderSeparator. Researching that is going on my todo list.
(of course SkeletonAttachment would make this super easy wink wink nudge)