I was more thinking that Lois as Kal-el's concubine might have tipped off Jimmy and Perry. However I guess it might not have been fully obvious to them why Lois showed up with Kal-el, so who knows. It's not like they were there on the ship.
What really blows my mind is how "Home is where the Hurt is" does not lead to Sam and Ellen figuring out something, or at least Ellen assuming her daughter is following in her father's unfaithful ways. There is a reason why there are stories on the archieve that explore these possibilities.
