Simply turning on "Use iCloud" within GoodNotes 5 is not quite enough to be able to store your data within iCloud Drive. The iCloud framework allows for syncing of data and backups to be made, however there are multiple facets of iCloud, and synced or backed up data do not always end up in the same locations. Adding on to this, confusingly "iCloud" and "iCloud Drive" also refer to two different things.
"iCloud" is a mechanism by which your app data is synced across all your Apple devices. If you have it enabled in GoodNotes on all your devices that are logged in with the same Apple ID, you should see the same GoodNotes data on all those devices (that is, your data is synced across all your devices). It's not possible to locate iCloud data; we only know it's safely stored on Apple's servers.
By contrast, "iCloud Drive" is Apple's cloud storage (like Dropbox, Google Drive, OneDrive) that is part of iCloud and counts toward your iCloud storage. To see your notes in iCloud Drive, you will need to manually export them to your iCloud Drive by choosing "Save to Files" after tapping Export in GoodNotes.
See also: Using Auto Backup to automatically create a copy of your documents in the cloud