Luke is his new angle on finally overthrowing the Emperor as per his offer to him on the gantry in Cloud City.
Vader is out in the feild when they discover that the name is Skywalker. That's why he's saying that he knows Skywalker is with them.
He didn't exactly want Palpatine to know he was already looking for him, because then Palpatine would question his loyalty.
He's just playing dumb to the Emperor that whole conversation. They both pretend that three of them could be a happy Sith family, but they both intend to replace the other with Luke.
That's why the Emperor pauses and repeats Yes... He's thinking about that to himself.
To me the biggest reason for this change was to make the Emperor consistant by having Ian playing him.
I guess I can see how the "how is that possible" helps smooth things over with the prequels by tying into what he thought happened to Padme and his potential children. I don't know to me it's basically the same scene with the consistant emperor.
Really the original monkey woman wasn't quite lame in it's own right. I can see why some of you even prefer that Emperor to the ROTJ version. But after really loving the way Ian played him in ROTJ (and now the prequels), the ESB version just sort of stuck out more to me.