I always assumed the Master Ball was never really featured in the anime mostly due to the moral issues it raises. The first time a Pokeball in the anime was able to capture a Pokemon without them being able to put up a fight, Mewtwo was controlling them, and it... wasn't presented in a very good light. The second time a "no-choice, no-fight" capture scenario comes up, it's at the hands of a legendary poacher. A Pokemon has to be able to battle, to earn the respect of the trainer, or something to that effect. It's the only excuse that keeps the stockholm syndrome-esque gray area of capturing pokemon leaning towards the positive.
As for Ultra Balls and such, I suppose it would be an arbitrary distinction that the animators and writers feel is unneeded.