I like your theory, and it makes a lot of sense because of the physical similarities between the Gerudo race and Demise, as well as their cultural differences from Hylians (for example, appearing to worship a separate Goddess for at least some time in the form of the Goddess of the Sand), and the fact thieving is their 'thing'. But there are in my opinion a few flaws to this: Ganondorf is a Gerudo, so referring to the Gerudo as a separate incarnation of Demise in some way doesn't really make any sense, as that pretty much falls into fact and not theory territory. Second of all, the Gerudo only really appear in 1 game, OoT (and MM of course but that is an alternate dimension), so it wouldn't really make any sense to say that Demise stating he would haunt their descendants means that he lives on within the Gerudo race.
Second, I always got the impression that the Gerudo were a tribe who relocated to the desert in Hyrule when they heard about the legend of the Triforce. That, or they were a travelling tribe of thieves anyway, perhaps coming from an alternate dimension (maybe Termina or somewhere else) or at least originating in another country, who settled in Hyrule for a few generations before moving on at the end of OoT when Ganondorf was defeated or alternative versions of this in the various splits of the timeline.
Another point that needs to be made is that it's not Demise being reincarnated himself in each game, but Demise's hatred being reborn. This would explain why other games have different enemies, such as Vaati, however it is all part of the repeating pattern in spite of this. Ganon is the same monster in both OoT and TP, for example, because he is not defeated but banished to a different realm between these games. This to me kind of makes it seem as if the Gerudo really aren't anything to do with Demise, aside from only appearing occasionally, because the reincarnation of Demise and his hatred appears in different forms in different games.
The other issue I have with the Gerudo being the incarnation of Demise is that not all Gerudo are inherently evil or pro the destruction of Hyrule in the process of seeking out the Triforce. Look at Nabooru- she was against Ganondorf from day one, and only supported him due to being brainwashed by Twinrova. If even one Gerudo doesn't seek the Triforce or seek evil, I think that is enough to suggest it is no more significant a race in Zelda than any other. Further to that, yes, they are thieves, but that is just their culture- it might be considered morally wrong by other cultures, but stealth and slyness are awarded in their culture as a form of intelligence and bravery, as seen by the fact they let Link have free passage when he releases the carpenters. That doesn't make them wrong in every way.
I think the fact only one male is born every hundred years is nothing to do with dark magic however. I really think that's just to make it more interesting, and explain why someone as evil as Ganondorf came to be in charge of the whole lot of them, and not someone much more respected and honourable such as Nabooru. I actually kind of look at the Gerudo race as a nod to feminism surviving within a patriarchal system of rule, because all of those women are tough fighters, keen horse riders, and live in a harsh climate. I don't think it has any real purpose other than to make things more interesting, the fact that there is only one male every century.
Twinrova do have dark powers, but so do all the other enemies in Zelda, including Ganondorf. There is magic throughout the Zelda universe, and far eastern culture such as Japanese and Chinese cultures include a focus on the balance of good and bad- thus there is good and bad magic. I don't think there is a source to it as it is an existent element in the Zelda universe. Magic has it's appeal in the fact it doesn't depend on the gods, it depends on personal skill, so it gives people free will to use it for good or bad in Zelda. I wouldn't think there is a real source in that case. Dark magic doesn't necessarily originate with Demise, because that would give it the eternal problem of oh but where did Demise get his power etc.
Sorry for the essay, your theory is highly original so it inspired me to think deep lol
