On a more serious note, I wonder whether it has something to do with the fact that on HN it is frowned upon to express agreement in comment form (that's what upvotes are for), however when disagreeing/expressing disapproval, it is accepted practice to explain why one disagrees (and rightly so in my opinion).
This could give the casual reader the impression that most of the interaction on HN is adversarial, simply because comments are more prominent than upvotes.
Interested to hear your thoughts on this dang.
Empty comments can be ok if they're positive. There's nothing wrong with submitting a comment saying just "Thanks." What we especially discourage are comments that are empty and negative—comments that are mere name-calling.
I joined HN fairly late (just a few years ago) and my subjective experience of the rules (as they are lived) is that a 'thanks' comment is almost invariably countered with a snarky 'that is what the upvote button is for' response.
For what it's worth, the vast majority of my experiences here on HN have been positive, and I greatly appreciate how often someone with significant domain knowledge turns up and replies to me in a way that seriously challenges beliefs which I had previously taken to be fact.