There were a few that I know of, in Marvel Comics anyway. Luke Cage and Jessica Jones had a baby that was kidnapped by Skrulls during the Secret Invasion series. Current status of baby is unknown to me. Vision and Scarlet Witch had twin boys, that I think were erased from existence. Not sure whatever happened with them. Cyclops had a baby with Jean Grey clone, Madelyne Pryor. He was infected with a techno-organic virus and sent to the future to survive it, lived a life in a post-apocalyptic future, then came back as Cable. Hmmmm... Oh! Reed and Sue Richards had son Franklin, who I think survived. So, based on that sampling... superheroes should never have kids.

I'm sure I missed a lot...