I might be making this up. But it seems that comments are disappearing here and there. I assume that they're just not up to snuff, but I haven't noticed other SE sites just deleting comments outright. (again, though, I might be dreaming this too...I've been known to not always pay attention ;)
I think this is my fault.
In general, comments can be removed for several reasons. The bigger sites tend to be more strict about this but we don't do a lot of comment pruning here.
Typical reasons for removal:
Rude or offensive
We really don't get comments that fall under this banner (or at least I haven't seen any).
Not constructive / off-topic
I've deleted 2 comments for this reason:
- A comment asking mods to clean up a comment thread. There really wasn't a reason to clean up the thread so I deleted his comment to avoid other mods wasting their time on it.
- A comment suggesting that another user was trolling. I did some research and found this assertion to be unsupported1 so I deleted it as noise.
I've deleted several comments in this category. If a comment references content that is no longer in the question/answer, it is usually removed to avoid confusion.
We have many comments that fit this description, but we're a growing community so I don't see a problem leaving them.
So yes, comments have been deleted. It's fairly rare, but comments get deleted when they distract from the real content.
1 The only "evidence" of trolling was the question asker's display name. However, the question content gave no indication of trolling; the user has accounts on other SE sites with many questions and answers and no evident instances of trolling; and the display name in question is a common dictionary word with no offensive meaning.