I do, then, immediately close "thank you" issues so owners are not tasked with responding in any way, but still... And for any watcher, I imagine they are interested in notifications relevant to actual issues, not thank yous.
My opinion is the current best way to say thank you is probably a star. Beyond that, it would be nice if GitHub added a way to leave a thank you or testimonial or something like that. Or even a formal "the repo is in use by such and such app/company."