The post you have replied to is over a year old now and this News post from June 2020 updates users with:
Support for system keychain on macOS and Windows
One of the issues mentioned in the security audit was that certain sensitive settings, like Nextcloud or encryption passwords were saved unencrypted in the Joplin profile. This new release will make use of the system keychain when it is available and move the sensitive settings to it. You don’t need to do anything to make use of this feature, it is automatically enabled in this release.
Currently this is supported on macOS and Windows. It is disabled of course for the portable version, and is also not currently enabled for Linux due to a build issue and less consistent support than on macOS and Windows.
(I have not looked to see if the Linux issue has also since been resolved)
With regards to E2EE, it is not a method of encrypting and securing the data on your local disk and never has been. It is there only to ensure that data transferred off your system to a cloud storage provider cannot be read by that storage provider or anyone who gains access that storage provider's systems. Of course it also provides protection in addition to HTTPS whilst in transit both to and from the storage provider.
From what I have seen, if you enable E2EE you will see two copies of each file in your resources folder; the "plain version", say 004864a886874b57a37cc6234760c448.png and the encrypted version, say, 004864a886874b57a37cc6234760c448.crypted which Joplin uses to send to the sync target. The notes in your local Joplin database are unencrypted and there are unencrypted resource files (attachments) in your local resources folder. However all notes and resources are stored encrypted on the sync target.
Local encryption has been raised many times in the past. This is just one of the many posts.
If you were thinking of requesting local encryption please have a search of this forum first as the pros & cons have been discussed many times. It is also somewhat covered in the FAQ.