I'm guessing that for so long as ultra beast cards get printed they will be tagged as "Ultra Beast" for the purpose of play and backwards compatibility even if more support for them doesn't get printed. New ultra beasts years down the road could be busted in expanded with the support that exists...
Blacephalon's GX does not count as taking a prize. Naganadel's GX does not add or subtract from the amount of prizes taken.
Example: My opponent takes 5 prizes. I Nag GX them. He takes 2 more prizes. He has taken 7 prizes even though 2 additional cards were placed down as prizes. Beastite would...
Maxie's and Archeops are both problems. Maxie's can get an Omastar or Kabutops into play turn 1. Archeops can easily be put into play by turn 2 and has no counters outside of Wobbuffet.