I should clarify that I don't think it's because it's because Japan is amazingly progressive about gender. (After all, this is the game where he gets groped by :biden-troll: who exclaims "You're... a man?!)
It's just that Japanese character designers can go "I think the dudes can and should be pretty too"
and then they lampooned it in MGS3 by having snake wear a bishounen face mask
They further dumped on Raiden in the form of Raikov. I never minded Raiden so both making fun of him in 3 and "fixing" him in 4 seemed unnecessary to me