Comments are not really intended for chit-chat. So, if you wish, you may flag comments that don't add any clarification are are purely social using the reason:
It's no longer needed.
This comment is outdated, conversational or not relevant to this post.
However, generic positive comments are not a significant impediment to the smooth operation of the Physics Stack Exchange site, and if they don't all get flagged and removed, it's that's not a big deal.
Moreover, I should also mention that different Stack Exchange sites can have different standards for thank-yous and similar positive comments on questions and answers. For example, on Science Fiction & Fantasy (where I am very active), expressions of thanks are fairly commonplace.