I don't think that either one of the knew that Jason was Superman's kid. Remember, Lois has no memory of having sex with Clark. She doesn't know that their relationship ever reached that level. All she knows is that she blacked out and ended up pregnant. The logical assumption there is that she was roofied and raped. Generally, that would preclude Superman, he doesn't need drugs to commit rape.
I think she'd have confided in Richard that she was pregnant and that she didn't have any memory of having sex with anyone around the appropriate time period. He'd also probably assume unknown rapist before even considering Superman.
At this point, I am wondering what the statute of limitations for rape is in Metropolis, and if they have a prison strong enough to hold him if Lois files a complaint.