This pattern is also sometimes called a doom box. They're useful for when you need to make forward progress on task #1 (tidying the desktop) but don't have the energy to do task #2 (actually deal with the random crap).
Having the proposed directory actually named "mess" is probably a much better idea than a semi-respectable sounding name like ".meta". A constant reminder that most of this stuff is a joke to begin with—that "none of this is necessary; it is merely customary", as Jef Raskin once put it—wouldn't be the worst thing in the world.
I've already thought about creating such a folder on my system. I'm happy to learn that I'm not alone :-)