I have yet to complete Dawnguard. If you do and side with Dawnguard do the vampire attacks on towns stop. I am having trouble where I go into a town vampires attack and I have to reload several times because they killed one of the shopkeepers. They somehow got Belethar in Whiterun when I wasn't there. I couldn't even find a body. All I got was an inheritance letter from a courier.

This has never been a problem for me... But I completed the Dawnguard DLC almost immediately after I got it. I haven't noticed any unusual vampire activity since beating it, though. It isn't uncommon that I'll find them out in the wilderness somewhere, but rarely attacking a town.

Yes, vampire attacks on towns and cities stop when you complete the main questline, regardless of which side you choose. You'll still see them in the wilderness at night, but never in the cities again. Unless, if you join the vampires, you use Auriel's Bow to eclipse the sun. That pretty much guarantees more attacks on towns, so be careful if you ever do that. If you block it out and stay in the wilderness till night or the next day again, though, you should be fine.

Edit @Jack Bauer: If you don't take them out quickly, they can be pretty deadly for the townsfolk. The guards can distract them for a bit, but there's usually a high level Master Vampire in the attack group, and he can do some damage. If you have the PC version, I recommend a mod called "When Vampires Attack" that will make everyone except guards hide indoors until the vampires are dealt with, saves a lot of lives. There's one by the same author for dragon attacks, too.

Scroll down to Violent Encounters

http://www.uesp.net/wiki/Skyrim:World_Interactions

Note, most Vampire encounters in the game, outside of the DG content are normal random encounters, and should not happen in towns or settlements. DG may have changed this.

What is curious is this statement from the Wiki

Random encounters with members from the opposing faction in hold capitals and the wilderness will be less frequent. Random vampire attacks will only occur during an eclipse.

Which basically says that the town attacks never stop with DG, even after the MQ. However i have never seen a town attack outside of DG MQ. Not sure if the Random attacks that always happened out in the woods still happen or only happen during an eclipse. Confusing to say the least.

Only time I've ever had hostile encounters with vampires in the wilderness without an eclipse was at night. Both before and after I completed the MQ.

I was getting so annoyed by having my cities attacked by the vampires and killing off valuable people that it basically forced me to play through DG just so I could make it all stop. After one of those attacks where they almost killed half the town, the guards would go walking by me and and say "We've got to do something about these vampire attacks" and I'd be like "You're telling me! They just killed like three or four merchants! This is getting RIDICULOUS!"

After completing the main DG storyline, the city/town vampire attacks stopped completely. There might be the late night wandering country ones once in a great while, but certainly no city attacks whatsoever.

Once the vampire attacks start ( usually around level 9) I concentrate on DG only until it's done.After that you only have normal vampire attacks.

I finished DG and yes, the vampire attacks on towns completely stopped, and the random encounters in the wilderness have trickled down to complete halt at this point for me. Mind you I joined the vampire hunters' side and have only beat it once so far.