I have a whole worldbuilding theory in my head regarding this very thing.
You see, I believe the Gossip Stone outside the Temple of Time in Ocarina of Time - the Gerudo sometimes come into Hyrule to look for boyfriends. Though an all ages/kid's game, this... gives a nice little implication that Gerudo mate with Hylian men - and given their "no men allowed!" culture, the relationships are probably very temporary, perhaps even one-night stand affairs. They probably mate with human (round-eared human) men if they're around, too, given similarities. I think that something in their genetics causes the offspring to have Gerudo-traits/to be Gerudo if female and human/Hylian if male.
I never thought of that possibility for Malon... if so, then, perhaps, some of the female babies are Hylian, as well, and the Gerudo only keep female offspring with the Gerudo-traits. Then, of course, once every century or so, the lone male with Gerudo traits is born (Ganondorf). In my mind, he is not only is the birthright king of their tribe, but it's "brood-stallion" existing to refresh and strengthen the Gerudo genetics. (When I write Ganondorf in fan fiction, I tend to make him used to getting whatever woman of his tribe he wants - a real harem-afficiando).
I also think that Gerudo like only those human/Hylian men who are "worthy" in their eyes... strong, good "stock." I.E. that is why the carpenters got locked up instead of lovin' - the ladies at the fortress probably thought of them as lazy, inferior stock, unworthy to contribute genes to Gerudo offspring.
I also think the Gerudo limit themselves to human/Hylians rather than say, going after Gorons or Zoras because of species/racial simliarity. Humans and Hylians are close enough to them genetics-wise to render viable offspring. Zoras, on the other hand, are an egg-laying/probably spawning fish-people and Gorons are made of rock!
