If they affect other instincts, they could definitely affect the sexual desire, or twist it.
Granted, nanomachines were taken to the extreme in MGS4, but a supernatural future, rather, superhuman, could achieve it's maximum efficiency only by individual cell control or a regulation of reactions in the nanoclimax. Nanos fit all the mumbo jumbo Kojima presents, because they can potentially do that. Were I asked to make a man immortal or control his thoughts, I'd try to create Nanos to do just that. Provided they are not thrown in my face every 20 seconds.
PSN Name: SSolidus (in the fridge right now) In Outer Heaven... Men Become Demons