I kind of assumed that it would get swept under the rug because working it into the story would be overly heart-wrenching.
Lois claiming to be the girl's aunt is a good deflection. It explains why she looks like her mother and lets her interact with the girl and be a family friend without the pressure of parental responsibility. When the kids are older and can understand the whole interdimensional travel thing, then Lois and Clark can explain why "Aunt Lolo" looks just like Mom.
The whole thing makes me wonder, though, whether the girl was told or understands that Clark is not the same Daddy she had before. Given her reaction to Lois, I expect that even if she was told that her parents died and that Clark is a "copy" of Daddy, she doesn't actually understand all that. It's a lot to dump on a 4-year-old. (Er, somehow I assumed she was 4, but going back and looking, you don't actually give an age. Meh, it's a lot for anyone, even if she's 2 or 3 or 5.)
And who better than Clark to take in kids who are not originally his and then accept that they're really his children? He of all people knows that a kid doesn't have to be born to their parents to be their kid.
