Don't get too hung up on the inbreeding. Pokemon don't even breed the same way that animals do in Real Life. Since " inbreeding " is already possible in the games, the offspring have no genetic defects, and many NPCs in the games claim no human has ever seen a Pokemon actually lay an egg it's possible that Pokemon Breeding is just different biologically then what we know as fact.
'sides the Lati@s breeding don't have to be (and probably are not) related. The pairs in the Main Games have never been stated to be related.