Isn't there a upper level limit of how many fid's the empeg can handle anyway? Won't that limit be hit soon by the amount of storage that you can stuff into the empeg>?

Yes, and, although I can't put a particular number on it, yes.

However, there's no reason to assume that version 3 software will have any such limitation at all. The empeg developers are aware of the problem, and they surely want the software to be as robust as possible, since it's intended to be used as a base for more products than just ours.