1) When the last boss is sealed in a bubble but just before popping it, pause the game and press select with the 2nd controller to bring them in (requires at least an extra life) then you can pop it.
2) You couldn't simply beat the last boss. You had to take the secret door in level 99 to some extra levels then beat all those. Incidentally you couldn't use only the level skip code(DDFFI, yes I still remember it) to go there, you had to actually enter the door.
Bubble Bobble was made back when you could pay game designers in LSD and cocaine.
It's a shame that Bubble Bobble was the high-point of the series... none of the sequels had the magic of the original. And the remakes were horrible.
Bub and Bob are now featured in about 400 derivative Bust-A-Move games.
Eat shit, asshole. Rainbow Islands is one of the best games ever made and Bubble Symphony and Bubble Memories are more-than-worthy successors to the Bubble Bobble throne.