To me, there are 2 issues here:
Comments that contain only "Thanks!" or "You're Welcome!"
Comments/questions that begin or end with the above.
I fully understand that #1 is mostly just a waste of space, although with a complete lack of ability to PM someone, it may be the best way to communicate appreciation.
It really bugs me, however, when I get a question edited only to find that the only change made was a removal of my tagline: "Thanks!". I always like to show that I'm appreciative of anyone taking the time to help me, and it seems super odd (and irritating) that someone would go out of their way to remove that, and only that, as "unnecessary".
I think minor comments can be too much at times (and we're all really here for the questions/answers), but within reason it's acceptable to me.
Anyway, that's my 2 cents.