Well according to recently sources Pokémon Bank apparently doesn't stop the majority of hacked Pokémon from getting transferred from B/W and B2/W2 to Pokémon X and Y.
It only stops Pokémon that have incorrect Abilities, Moves and Stats etc. This is what Pokémon Bank apparently considers to be hacked Pokémon:
Before you say anything there is evidence to support this since it has let Pokémon such as these be transferred:
This Tepig is considered to be hacked since it's Thick Fat Hidden Ability hasn't been released yet.
Totodile in a Master Ball, Seriously?
This Torterra is Illegal because it has it's Hidden Ability and is Shiny.
Anyway by the evidence presented in these sources, I can safely say you should be able to transfer your Pokémon over with no problem.
Regarding your other question:
Yes. If you hacked your game to have 999 Master Balls, any Pokémon you catch in them will still be able to compete in Tournaments.
I did the exact same thing on White to get 999 of every item, battle item and berry. I caught half of my Pokémon with the hacked Master Balls and was still able to compete in the Official Tournaments with them.
Overall Sources: http://tay.kotaku.com/pokebank-hilariously-fails-to-stop-hacked-pokemon-1489449874