Newsarama managed to ask Bryan Singer the $10K question: since Clark erased Lois’s memory of sleeping together in Superman II, does she not know how she got pregnant? Here’s Singer’s response:
NRAMA: After he gave up his powers in Superman II, Lois and Superman slept together. I’m going to assume that that’s when he got her pregnant…
NRAMA: Then he gives her the kiss, which made her forget that they even slept together. Was the pregnancy a mystery for her?
BS: I ignored that part. I just assumed she remembered sleeping with him.
So there you go. Just ignore that part! But wait—does that mean Lois knows Clark is Superman? I guess you should ignore that too.
The rest of the interview is primarily Singer stating his opinion that poor marketing is the reason for Superman Returns‘s relatively unimpressive box office numbers.