Hi b,
Probably better to post this type of message (a request for tech help) in a thread separate from this one (arguing the merits and demerits of autosave/versions, etc.)
The new feature that' bugging you is "resume", a feature that assumes anything you left open is something you're not finished with. Because you're not finished with it, Resume opens it the next time you launch its application so that you can continue working on that file.
Avoiding that popup is something your mother (and your kindergarten teacher) told you (many times, if you're like me): "If you're done with your toys, put them away."
Translated to the current situation: "If you're finished with that file (for now), close the file before you quit Numbers." Do that, and Resume knows you're done with the file (for now), and won't open it when you next launch Numbers.
Same for Pages, but this thread is in the Numbers community, so I've referred to Numbers here.
Regards,
Barry