a comment where I said "thanks" when somebody pointed out a formatting error in my comments is now at -1.
That sounds like a pretty low value comment. Is it beneficial to third parties to be able to read it? If not, just make the correction and PM your thanks. Otherwise you're unnecessarily wasting everyone's time in the guise of politeness.
I think saying thanks is public for corrections contributes to a courteous atmosphere. It encourages third parties to make and accept corrections.
If such thanks were getting to be a drag on discussion, I'd recommend a different policy, but I don't think we're at that point.
If it's worth saying, but not worth its own post (even in Discussion), then it goes here.