I'm pretty sure Legendaries have genders, y'know, aside from Latios and Latias, the anime has shown them to be able to breed (Lugia), I mean these are legendary creatures so there wouldn't be anyone to study them to find out what their genders are, I'm pretty sure it's said somewhere in X&Y that some Pokemons genders are just unknown.

There are a few that just look like a male or female, others couldn't possibly have genders, like the Regis or Arceus.

But if you yourself were to assign a gender to some legendaries, what would they be?