I've already read this: Official reference for “don't leave ‘thank you’ comments”
Some comments are not very helpful because all they say is: thanks. The system could detect this word in the comment (and other sentences like "thank you", "ty", etc) and suggest the commenter to click on the thanks button, instead. This button would be semantically different from the upvote button, in that it would mean that the question was not particularly helpful, but the commenter wants to thank the answerer.
Thanks-votes may or may not contribute to one's reputation.