After all, they have the combined experience of several lifetimes at their disposal, so it’s not hard to believe the mutants could avoid detection until they chose to make themselves known.
It’s kind of messed up they wouldn’t attempt to lend a hand with Thanos, though it’s worth noting the mutants in House of X tend to look out for their own above all else.
Plus, House of X creates an actual reality where mutants exist and could be flying under the radar on a level that even a group as informed as The Avengers may not be aware of their existence.