It is most likely a dragon attack. Check the area surrounding the city for their corpses. If you find them dead, and play on the PC, then you can use the console to resurrect them.
To resurrect an npc (enemy or friendly), walk up to them, open the console, click on their corpse (you'll see an npc code pop up in the center of the screen), then type resurrect and hit enter. They'll pop right up like nothing happened. If they're hostile, they will attack you.
If they don't pop right up after that, you probably misclicked their corpse, and got an item code for something near them. In this case, try clicking around till you get a different code, then try to resurrect them again.
Edit: Be careful when using placeatme as @agf suggested, it has created duplicate npc's in the past. You can get rid of these by selecting the unwanted npc while in the console window and then typing disable -> enter.