If the emulator can’t run games from archive files, then I store what I play unarchived, and what I don’t play stays as archived as it was.
Unless they’re small files, then I’d probably back then up extracted. But I haven’t had a case where the files were small enough for me to store extracted but the emulator couldn’t run from archives.
Just because you added a question mark doesn’t mean it fits this sub. I think this post isn’t at all in line with what the sub is about.