Clark's never been all that bright about personal things.
Maybe he doesn't know that births can come not only earlier but also later than expected.
Well, in Monte Cristo, the boy *was* Mercedes's husband's son and there was the duel problem: will Monte Crisrto harm Mercedes's son in order to avenge to his father?
I remember one fanfic where the Kryptonian gestation time was six months, so poor Lois thought her child was Lex's when it actually was Clark's.