JEX is a tar file but tarballs are not compressed archives. Could the smaller size be because the JEX file does not contain historic note versions and their associated resources (if they are not also being used by current notes)?
I suspect yes. While attempting to clean Joplin Cloud, I ran into issues.
Used a first-party plugin intended to clean sync target to which user doesn't have filesystem access. Not realizing that the plugin cleans Notes, Folders, Resources, and Tags, but not NoteTags, Master Keys, and Revisions.
Then created a new Master Password, which generated a new Master Key. As old Master Keys remained on Cloud, sync returned the old Master Keys to my client. Sync also added the new Master Key to the growing collection of Keys on Cloud. Now there are old Master Keys requiring the old Master Password. And a new Master Key requiring the new Master Password. And as far as I can tell, I can't do in Joplin Cloud the equivalent of rm -rf <sync-target>, so I'm stuck with all of them
Long story short, I haven't yet been able to see what Cloud storage use would look like after a clean upload.