The "GoodNotes" size in your device Settings > Apple ID > iCloud > Manage Storage refers to the total size of your GoodNotes documents in iCloud. Therefore, if you see "GoodNotes 5" on this list, it means you have some GoodNotes documents in iCloud. Tapping "GoodNotes 5" and choosing "Delete Data..." will free up some iCloud storage, but contrary to the warning, the local data will not be deleted from the app. When you open GoodNotes again, you'll have the option to upload your data back to iCloud.
The other "GoodNotes" size in iCloud Storage > Backups > "This iPad" refers to the total size of the app, that is, the app size plus its documents and data (including deleted items in GoodNotes Trash Bin and all temporary files), which explains the larger size. If you disable "GoodNotes" here, your GoodNotes documents in iCloud won't be affected. It just means that your device will not automatically back up the app to iCloud, and so in case you want to restore your device, "GoodNotes 5" will not appear on the Home Screen until you redownload it manually from the App Store. If you're running low on iCloud storage, you can certainly disable "GoodNotes 5" to free up that space in iCloud.