The only point of Concern I’d have is if said hacked Pokémon had an illegal ball for the offspring that got passed on by breeding. The most obvious example would be anything not featured in Hisui having a Strange Ball (meaning it has a Legends: Arceus Ball Type). However, they pass down as Pokeballs through breeding.
You wouldn’t have to worry about Cherish Balls and Master Balls either as they also pass down as Pokeballs through breeding, which most Pokémon that can breed, if not all, are legal in. :P