I think that's hardly enough evidence to say that Cyclops definitely knew the truth. It's possible... but it's still ambiguous at best.
And yes, we know when he left relative to Spoiler: Lois' getting pregnant, but we don't know where that actually falls compared to the events of Superman II... or any other Superman movie. I don't think it's implied that he Spoiler: got her pregnant during Superman II, so who knows how long after Zod that that actually happened.
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