Are you kidding? Come on, they can't be lesbian with each other. They're twin sisters for crying out loud! Come on....
I'm sure Ganondorf was born of both a man and a woman. His father was probably the previous male Gerudo. Maybe the father dies or is even ritually killed when the next male is born. There's really not enough information on it, though Din wrote
a very interesting article on it for those who might want to consider the finer details of Gerudo bilogy possibilities. :>
In any case, something must've happened to his parents for Koume and Kotake to raise him like he is theirs. They seem more like minions than parents though so maybe they knew something about his destiny and that is why they decided to be the ones to raise him? Who knows! >_<