This is not easy to do with Finder. If you happen to have a copy of PathFinder you can manage to index the folder. Apple applies several misdirections to keep you away from certain folders related to iCloud.
To index your iBooks folder using PathFinder, navigate to ~Library > Mobile Documents > iBooks > iBooks Confusingly, macOS makes it appear that there are three iBooks/iBooks folders. Just poke around until you find the right one. (ForkLift is less-expensive option that works for this purpose also.)
When you find the folder that actually contains your books and PDFs, ⌥⌘-drag that folder to your DEVONthink database to index it.
THERE ARE DRAGONS HERE. macOS’s management of iCloud data is not meant to be hacked by you and me. Sync glitches, or changes to macOS, or other hazards might cause you trouble. So NEVER change the content of the folder. Look but don’t touch.
It’s probably better to use Hazel to make a mirror of the iBooks folder to some ordinary folder that is not so fraught and index that mirror folder.