There are baby versions of Amaterasu, Ushiwaka, and all of the brush gods. If the developers didn't intend this game to be cuteness for cuteness's sake, I don't know what to believe in anymore.

I was confused at first because a lot of comments suggested that Kurou was Waka's son, but then I found a recently-made short comic that the artist marked for spoilers. It was Waka placing Kurou in a rocket, which -- as it apparently happened before the game, and thus wasn't actually shown -- the artist drew to resemble Kaguya's. He mentioned how Kurou, being Waka's "duplicate," could be thought of both his brother and his son. Long story short: I think you're right about the clone thing.