Yeah, it's implied that the Gerudo and Hylians interbreed. I'm sure some of the more elite Gerudo 'get busy' with their current king, but yeah...Talk to Talon with the Gerudo Mask on in OoT, he says it looks like Malon's mom.

How that doesn't make the Gerudo bloodline die out over time, I don't know. If Malon's any evidence, maybe only the children who look more like Gerudo than Hylians join the tribe or something.

As for the Kokiri, I always imagined the hatched from the Deku Tree's seeds as babies like it was an egg or something, and grew until they were about 10, where they stopped. How that makes Kokiri able to have ancestors (ala Mkar descended from Fado), I dunno. Maybe the Deku Tree mixes physical aspects of two Kokiri to make a new one?

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