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.