Well, Vivec is destroyed ofcourse. I don't know about Mournhold though... It depends on how far into morrowind the lizards got. And wether people from southern morrowind fled to Mournhold, or people from Mournhold were fleeing for the onmarching Argonians.
According to the game, Whiterun would be the biggest city in Skyrim, but plagued by war and the fact that Skyrim is a rather uncomfortable place to live, I doubt wether any city in Skyrim would be among the most populated. I know nothing about Senchal though. But I can't imagine it to have more inhabitants then places like the IC or Wayrest.
That's true. I didn't really take the present situation of Morrowind into account when writing that. As for Whiterun, I find it a bit strange, since it's never been the capital of Skyrim (to my knowledge), though it is a trading hub because of its central position so it would make some sense.
I just remember reading in the first edition of The Pocket Guide to The Empire that Senchal covered all of the eastern tip of the ''Something-Something''-Peninsula of southern Elsweyr. And it gave me the impression that it was rather large, despite the fact that most of it was mostly slum. However, it's not as big as IC or Wayrest as you say. That's rather obvious.