To add to Wals reply.
Any book in the device view WITH a tick mark , also has a Tick in the main library.
So, You can add a tag
You just have to switch views. (click the column head to sort or enter the search: ondevice:true then do a bulk edit and Add Tag
BTW Only those WITHOUT a tick in device view, do not exist in the main Library (you might want to select those and right-click "copy to Library" as a backup )