So... in Tears of the kingdom the Gerudo is hit with a regional phenomenon of a sand shroud and mummy-like monsters known as the Gibdos. Now the Gibdos have a very similar appearance to the gerudo. In tears of the kingdom there is an underground cemetery in the depths under the gerudo dessert. In breath of the wild we technically have entrances to the depths for example the "bottomless" pits at the yiga clan hideout and at the gerudo tower, it's just the gloom hasn't had a large effect yet. So my theory is that the gerudo knew about the depths and decided to do explorations of them. We know that without Zonai devices, shrines, and ascend there's no way out of the depths. The reason there is an underground cemetery is because when the gerudo explorers died they were buried in the depths which is why the cemetery is full of Gibdos. Since ganondorf is a gerudo male which are only born every 100 years he draws his power from the depths. So when ganondorf caused the openings of the depths in doing so brought back the buried gerudo in the depths from the exploration.
