It would appear that Gerudo women still need men to reproduce, so they seek out husbands. Apparently this can include Gorons and Zoras one wandering Gerudo you meet on the roads in Hyrule says she doesn't care if her true love has gills, etc. (I suppose she could just be looking for true love rather than to start a family. Not that those two concepts can't be one and the same, of course.)
It might simply be the case that any humanoid race in Hyrule can have kids together. Whatever the case, OoT established that there's only one male Gerudo born every 100 years (if that), so the Gerudo would face extinction if not for procreating with other races.
The Zelda games, being fantasy, don't really have to bind themselves to the same biological realities we face. What I appreciate is the humanizing element they have by focusing on the intelligent soul shared by all of these species/races. It doesn't matter what they look like, because they all think and feel the same. It's a lesson the whole world would benefit by learning now.
To circle back to your other concern, about how we'd react if the shoe were on the other foot and it was a male-only town and women weren't allowed:
It's hard to say how that would appear without the proper context. But Gerudo Town is refreshing, in part, because women still struggle for equality alongside men in the workplace, in our own hobby all sorts of contexts. So it's encouraging to see the power dynamic shifted in this way.
Also, there's a potential story justification in how the Gerudo marry and reproduce in other lands meaning they might be assimilated into other cultures and lose their own culture. Having a town that raises Gerudo (which are all female) while they're young, and without male interference ensures that the culture is taught and preserved, and then passed on when a Gerudo woman has her child and presumably takes them back to Gerudo Town to repeat the cycle.
I think it also feels OK because the Gerudo women don't have any problem with men. They're merely honoring a tradition.
It's nothing personal, and I'm sure they'd help out if, say, a man passed out from heat exhaustion at their gate. Riju and the other Gerudo all seem like good-hearted people.