While it is true that some do have no cities and others have two, I think there's another possible solution. If I'm not mistaken, most Dukes in this stage of the game are also a region lord in that Duchy. You could then make that region be considered a Ducal Seat. Any regions too far away from that Seat would not want to listen to the Duke anyway.
Another possibility is that the Ducal Seat has to be "declared" like a capitol. When you create a duchy, you do so with one region typically and then have the regions join. That first region would be the de facto Ducal Seat. They could move it to another region by going there and have a "cost" similar to moving the capitol. Could even throw in some sort of bonus to loyalty or what not if the Duke visits the Ducal Seat.
Just random musings...
