As far as I can tell, it's not possible to thank edits made by bot users. On the desktop site, the thank link doesn't show up, and attempting to do it on mobile gives a rather unhelpful error message: "Thank action failed. Please try again." This button should be hidden in this case, or else a better error message used.
Related Gerrit Patches:
|mediawiki/extensions/Thanks : master||Hide thanks button for botedits if bots are not allowed to receive thanks in mobile as well|