The "Goodnotes" size in your device Settings > Apple Account > iCloud > Storage shows the total size of your Goodnotes documents stored in iCloud. If you see Goodnotes listed, you have documents saved there. If on this page you choose Goodnotes > Delete Data from iCloud, it will free up iCloud space but won't delete your local Goodnotes files. When you reopen Goodnotes, you can choose to upload your data back to iCloud.
The storage shown in Settings > Apple Account > iCloud > iCloud Backup > This iPad includes the app and your documents. Disabling "Goodnotes" here won't affect your Goodnotes documents in iCloud or your local Goodnotes library. It just stops backing up the app to iCloud, so if you restore your device, "Goodnotes" won't appear on the Home Screen until you redownload it from the App Store. You can safely disable it to free up iCloud storage if needed:
Then there's another storage size shown in device Settings > General > iPad Storage. It includes the storage taken up by the app + your documents + its temporary files: