iCloud has many parts, and the Files portion represents what is saved in iCloud Drive only. Backups and backed up app data are not in iCloud Drive, they are in iCloud, along with iCloud-sync'd data like Contacts, Calendars, etc.
The Whatsapp data should have been deleted when you tapped on it and then tapped on Delete Data. If it is still showing some data, then you can try deleting it again, and if it does not remove it, then try resetting your device:
On an iPhone X, iPhone 8, or iPhone 8 Plus: Press and quickly release the Volume Up button. Press and quickly release the Volume Down button. Then, press and hold the Side button until you see the Apple logo.
See if that removes the line item from the list altogether. If it doesn't, post back, as you may need to back up your device and then restore it to see if that will clean up the hanging threads.
Here is a User Tip on iCloud and its various parts. It might be a good idea to take a look at it because it explains what each of the different pieces of iCloud do as well as what you can and cannot see in iCloud: iCloud Deconstructed | Communities
Best of luck,