I've purchased a Clara 2E for the better half and am slowly setting it up before wrapping it up for Christmas. I have a Clara HD myself.
I've noticed that the Clara 2E has a large number of collections based on my tags with 0 books.
I checked and in Calibre I had both KoboTouch and KoboTouchExtended enabled. I've now disabled KoboTouch.
On KTE I had it set to 'Delete empty bookshelves'. I did not have KT set that way. I disabled KT, plugged the 2E back in and ejected it and still have the empty collections.
On Metadata, on device & advanced, I do have Update metadata on the device checked.
Does it take a while for them to disappear? Do I have to sideload another book or manually refresh metadata or anything like that to clear them out?
(Incidentally, I did search and found these two threads, but the info appears to be outdated:
How do I delete empty collections?,
Empty collections)