I'm pretty certain that the Gerudos breed the good ol' fashioned human way. This evidence is supported by a Gossip Stone that tells you that the Gerudos go to Castle Town to pick boyfriends (yes I know this has been said like 396903469438 times before, but I think it just needed saying before.) I'm certain that Gerudos aren't Cloned. That would require some sort of technology which is only just coming to light in the modern world. It's use in a game set in medievil times would be... very silly.
I also think it is very unlikely there is any kind of stork involved. If there were a Stork, there would be no reason as to why there was only ever 1 male born every 100 years.
However, I have just thought of a mild theory. It is probably stupid though as I am very tired. What if, the Gerudos go to Castle Town, and mate. Then when the baby is born, they take it back with them, and perform some sort of 'initiation' to make it a Gerudo. IF one male is 'Born' a year, maybe they consider their 'birth' as a Gerudo their initiation. This way, no males would be 'born' until the last male (their current king) is dead. This is because the king would not chose ANY males to be initiated as if some males were, there would be a chance that they would steal his throne. So, what I am basically getting at here, is what if the Gerudos use the term, 'Born' technically, as oppose to literally?