Heh, it's true they never address the fact that that Naomi came from another Voyager. But I think if that did bother Sam it would have been right after she was born. Technically she is her daughter, the same girl she carried in her womb up until the point of the split, a few hours before she was born. Same genetic material, that is her daughter. Once the emotional bonding occurred I don't think a mother would care anymore.
We shouldn't read too much into Neelix hanging around the Wildmans. He's the logical choice for a crew member to interact with any children, he's the right balance of outgoing and empathetic.