That was sweet.

As for the whose baby it is, I think we basically know that it is Clark's.

(1)Luthor used a condum, they didn't use protection.
(2)Lois's pregnacy was harder than Lucy's, which indicates it's part Krytonian.
(3)They said the baby looks like Clark.

But even if they were to do a DNA test (from STAR Labs or something), what then? If it turns out that it is Clark's baby, it's fine. But what if it turns out to be Luthor's? How would they treat the child? Would Lois want to persue adoption even though Clark wants to keep the baby? I think they believe it's better for them not to know and assume that it's Clark's. Besides, it is their baby to raise.