I have a bit of a theory on this one as well. My thoughts stem from my childhood, back when I didn't know what the term "surrogate" meant. I always viewed Kotake's and Koume's fused form (Twinrova I think. I can't remember if that's the name of their fusion or a collective name for the two of them, but I'm using it as the former for distiction between the three beings) as Ganondorf's mother. Now that I'm a bit smarter, I've managed to work that thought into a theory that makes quite a bit sense (to me at least): Twinrova, their fused form,
is Ganondorf's mother, and the two as seperate beings would be surrogate mothers since Kotake and Koume as individuals both technically are and are not his mother. I did a bit of digging to back this up, and I found something interesting in Navi's comments.
Navi states for Kotake and Koume: "Ganondorf's surrogate mother. Sorceress of (Ice/Flame). She seems vulnerable to (high/low) temperatures." (Note: Kotake's comment uses the first word surrounded by parentheses and Koume's uses the second).
For Twinrova, Navi says this: "This is the combined form of Kotake and Koume. Turn their magic attack back at them!"
Notice that as soon as the two fuse together, Navi completely drops the surrogate mother comment. I believe the reason for this is that Twinrova is not Ganondorf's surrogate mother, but his actual mother.
The better question: If there is only a male once every generation, who would his FATHER be?
As for this, there is a Gossip Stone somewhere that basically answers this question for you. It states, "They say that Gerudo sometimes come to Hyrule Castle Town to look for boyfriends". So that answers that.