I've edited and flagged a lot of questions and comments. Most often to remove "Thank you", "Thanks in advance", etc. One is actively encouraged to remove this fluff (Should 'Hi', 'thanks', taglines, and salutations be removed from posts?).
Why not notifying users that writing "Thank you" is not necessary? My idea: Whenever someone writes "Thank you" in a question or comment, a bubble could show up saying that it's not necessary, maybe with a link to a site explaining the etiquette on the SE network.
This could prevent a lot of work and take load off from the moderators.