LexX said:

In my opinion Yoda and the emperor do know about each other and that's also mentioned in the novelization of ROTJ.

Also I never liked Yoda when I was a kid but after they made him even worse for the prequels which I'm now trying to forget forever, I've grown to like him more.

when watching ROTJ you also get the impression yoda knows the emperor. Yoda tells luke to not underestimate the powers of the emperor or suffer his fathers fate he would. That tells you that they knew or know of one another.