Both a verification of the inbox is successful and a search for item:pending doesn’t find anything? This is indeed weird.
But if the inbox is really empty and the sync location was cleaned successfully, then you could try to quit DEVONthink 3, delete ~/Library/Application Support/DEVONthink 3/Inbox.dtBase2 and launch it again to create a fresh inbox.
Or do you also synchronize via Bonjour?