> There's nothing wrong with submitting a comment saying just "Thanks."
I'm pretty sure they meant saying "Thanks." in response to another comment, not as a top-level comment reply to a Show HN.
Kind of like how you wouldn't bust into a restaurant and say a loud "Thanks." to the entire room, despite it being perfectly fine to say thanks in a restaurant.
You can see the this covered in the mod comments, toplevel positive fluff is fine. Most of it doesn't go anywhere (as in, it's not like these end up the top of the thread and collect fluffreplies) and are, at a minimum, not worth policing.