Hi. My sim recently discovered a patient of hers was an alien. He was wearing his human "disguise". She had twins with him but they came out with normal skin color and none of the hybrid alien feature...
You should be able to have a parent click on the child and help them remove their disguise if they have one. Unfortunately, I've never had a natural alien (not a CAS one) have children so I don't know if its normal for the children of a half alien, half human to not be part alien. :(