Yeah well, when the truth more or less comes out we'll all look like morons in retrospect.
If Tywin was fucking Shae in front of Tyrion or somehow knew that Tyrion would find out, then sure, maybe he was doing it as a fuck you to Tyrion. But he wasn't. Tyrion never would have known about that. And Tywin is not Cersei, he isn;t stupid, I'm sure he knows that Tyrion didn't kill Joffrey. He probably just doesn't give a fuck. He despises Tyrion, he is disgusted by him, which is why it is hard to imagine him taking Tyrion's seconds.
The big indicator, to me, is the necklace. Ok, so Tywin fucks her. Crazy out of character, but ok, a man has to have his nut. Tywin allowing his hated son's whore to wear the insignia of The Hand? That shit implies some deeper feelings or connection. No way in hell Tywin "fell" for Shae. If the theory is that Shae was always with Tywin and she was using Tyrion the whole time towards Tywin's ends... very doubtful, but to me more believable than Tywin catching feelings.