Did you delete the thumbnail caches as well?
Yes, I deleted everything in my Thumbnails folder (as I mentioned in the first post).
Try launching the game once without any CC. Check that the catalogue is clean, load the game again with your CC and the empty slots should be gone. It worked for empty CAS thumbnails I had. If they're still there it's overrides you forgot to remove, things like recategorizers or to make an item shiftable.
After reading this, I realized I still had some stencil overrides installed, from here at MATY.
*facepalm So I uninstalled those and will try your suggestion.