When Assets moves files around because of dynamic Assets folder changes, it does not remove empty folders.
On the surface it seems like a no-brainer - just check if the folder is empty and if so, then nuke it! But if you go deeper, it gets complicated.
Should the physical folder be removed as well? If not, then the next time you index Assets, the folder will be reinstated. If yes, then what to do if there are unindexed files in there? Remove anyway? That's destructive. Don't remove? Then that makes Craft behave differently based on something that is out of its scope. What would users want in this case? Who knows!
You see, it's a bit tricky especially in terms of what the users would expect out of that functionality, so we just instead decided to go with leaving empty folder, as the folder path changing should not be that often of an occurrence and does not set us up for complex support tickets down the road.