Hi there!

Almost every time a dragon attacks a city some npcs die during the attack resulting in me getting his last will delivered. The same happens since I got the Dawnguard dlc with the vampire attacks. Is it possible that those attacks eventually clear the cities from npcs? Doesn't it affect quests or something?

thanks for help!

It is possible, and yes it does affect quests. Many times I have had a 'miscellaneous' objective no longer obtainable because Sven died, or Ysolda, etc. I don't have Dawnguard, but every time an Elder Dragon attacks Riverwood I lose somebody (unfortunately not Delphine...)