Possible spoilers...
-------------------------------------
I believe the Gerudo were wiped out. My reasoning for this is as follows: Tetra states, as she and Link approach the Forsaken Fortress for the first time, that the Fortress used to be home to another band of pirates, "but they were only small time." This leads me to believe that she is referring to the Forsaken Fortress as being the Gerudo Fortress, which would make sense, since its now the hideout of Gannondorf, of the Gerudos. Perhaps the Gerudo females couldn't survive the flood or whatever. Anyway, there's my thoughts.