Can you please consider the fact that they take boyfriends, the most likely scenario for the Gerudo is that they abandoned Hyrule for a while, possibly because of a war.
It would make sense that perhaps some of the Gerudo women did decide to integrate into the Hyrule Kingdom, but I believe some of them just moved. They probably were a little embarrassed by Ganondorf coming out of their group and felt a bit of shame, so they decided to just go away. A few posts ago someone suggested that they were transformed into the Twili, I don't believe this is the case at all. It is not the Women's fault hat Ganondorf did all the bad stuff.
MM takes place in a different world in ways... so not really the same people... However ... what happened to the Gerudo? If I were to guess... they go tired of living in the hot desert and moved into main parts of Hyrule... Saying that the Gerudo are not evil... so why won't they be able to come to Hyrule?