The three other cities may be smaller (or maybe destroyed like Kvatch :huh:). Don't expect them to come in DLCs.
That's what I'm expecting. There are two different ways to obliterate a city. The first is to imagine a horror verson of How To Train Your Dragon. A bunch of dragons sweep down and blast everyone to hell. The second plausible way to destroy three cities is to remember that there's a civil war going on in Skyrim.
Edit: About the Morrowind cities, I think that only Vivec, Ald'ruhn and Balmora were large cities. The other were like smaller towns, and there were lots of them.
There are three great houses represented on Vvardenfell: Hlaalu, Redoran, and Telvanni. Each one has an associated major city: Balmore, Ald'ruhn, Sadrith Mora. Then there is of course Vivec. During Tribunal, they added Mournhold, thus bringing the total number up to 5.