If you have two iOS devices, I would compare the Settings - iCloud - Storage - Manage Storage screens to ensure both agree. One device can get stale or cached data. If you don't have two, restart your device to check that it's updated.
If so, you will then want to go to iCloud.com on a computer and verify the number there. The web app allows you to clean or observe the rest of the backups. They are deleted photo albums (potentially) as well as backups of calendar, contacts, files and bookmarks.
IF at that point, you still think there's something missing - you'll want to escalate to Apple Support to http://apple.com/support/icloud
Doesn't look like there's a way to single out the Desktop via the 'Manage Storage' GUI.
However, you can always just symlink any directory from your iCloud drive; that way you can ensure that only the Desktop folder is being synced. This is with the caveat that while your Desktop files are being stored in iCloud, they're still taking up space on your HD before, during, and after sync. If you do it on every Mac then you'll keep your Desktop in sync between them all (files added, deleted, changed etc); this might not be what you're after though.
If symlinking isn't something you know how to do, instructions are below.
Backup (via TimeMachine or whatever you use).
Then fire up Terminal and run the following to move your Desktop folder into your iCloud Drive:
mv ~/Desktop /Users/<yourusername>/Library/Mobile\ Documents/com~apple~CloudDocs/
Then just symlink it to the usual 'Desktop' location:
ln -s /Users/<yourusername>/Library/Mobile\ Documents/com~apple~CloudDocs/Desktop /Users/<yourusername>/Desktop
Now anything that you add to ~/Desktop (by dropping things onto your desktop etc) will actually be dropped into your iCloud drive. They are of course still taking up local space on your machine. When you delete something from your desktop then it's gone from the 'Cloud' as well. The benefits of this are more for sync between machines (+ access via your iPhone of course).
If you've got another mac, move anything you value from it's desktop folder into your iCloud Drive 'Desktop' folder first, then delete ~/Desktop on that machine and symlink again as above.
Best Answer
Yes Spotlight is indexing iCloud Drive. It could take a while before your iCloud Drive is indexed.
Spotlight even shows if the file you are looking for is located in iCloud Drive.
To test if the metadata is still working after the file is purged I did: