I don't think Clemenza making the smartass comment about Paulie being a dance judge indicates any doubt on Clemenza's part about Paulie. I think it's merely a line of dialogue insterted simply so that scene had some dialogue. If you wanted to infer that the line meant to show Clemenza's jolly old fat man side, I can understand that, but, IMO, nothing more. If Clemenza had any doubts about Paulie, there is no way he would hold any job within the family, much less a job as important as Vito's bodyguard.

As far as Fredo not being a made man because of anything written in GFR, after having finally read it just so I can see how terrible it actually was, all I can say is .