In the modern comic version of Superman it took years before Clark/Kal-El's body soaked up enough sunlight to give him powers. In SR they even showed him finally discovering his powers as a teenager. So Lois carrying a baby for a few months wouldn't cause her any health problems. Also, I think Superman has to think about using his powers since while he is Clark he doesn't go around destroying things like a out of control Hulk so maybe his sperm isn't high energy especially if it is like human sperm and has a short shelf life which doesn't give it's cells much time to soak in sunlight.
It's not like Clark is a woman who carries the same number of eggs around her whole life which would then have the chance to before "superpowered". So maybe it's harder to get a female kryptonian pregnant since human sperm wouldn't be able to attach to a "super egg".