I am using extensions in Safari with no issues and yours is the first post I recall seeing on this, so I doubt it is El Capitan causing this.
You still have not answered my question if you have tried a safe mode boot then reinstall the extensions to see if they persist.
I am having a similar problem with Safari Extensions disappearing after a log-out/restart but not a simple quitting of Safari.
First, some background. This started when my work installed a product called Centrify that basically requires us to use our Badge to log into our computer buy deleting our Login Keychain and moving all of those items to a Token Protected keychain that is unlocked by our badge. At the time, I was on El Capitan on a 2012 MacBook Pro. Recently got a new 2017 Mac Book Pro with Sierra (clean install) and the problem persists.
I can install extensions and they remain in the menu bar of Safari, working normally, until I log out of my account or restart. Upon logging back in, the extensions no long appear and in addition, my Start Up page settings get reset to the default Apple page.
I can reinstall the extensions and reset the startup page and all is well until the next logout.
I have verified that the actual extensions are not getting deleted as I can go to ~/Library/Safari/Extensions and there will be, usually, multiple copies of each extension. So, although the extensions are not getting deleted, Safari is loosing knowledge of them after a restart.
Based on your post, I looked into ~/Library/Safari/LocalStorage and I do not have any files that start with “safari-extension_com”. Of course, this may be due to a change from El Cap to Sierra but I did not know to check this folder at that time.
I then tried an experiment.
-I deleted one of my extensions using the Safari preferences.
-I quit Safari.
-I restarted Safari to verify that extension was not showing in Safari.
-I re-installed that extension.
-I went to ~/Library/Safari/LocalStorage to see any changes and there were now three new files
https_safari-extension.apple.com_0.localstorage
https_safari-extension.apple.com_0.localstorage-shm
https_safari-extension.apple.com_0.localstorage-wal
-I then quit Safari (did not log out)
-I restarted Safari and went back to ~/Library/Safari/LocalStorage and the three files are gone.
UPDATE: I just realized that these three files disappear when I simply close the Safari Extensions window, not just when I quit Safari. So, may be unrelated.
So, any ideas on where the ‘existence’ of extensions is stored so that Safari know about them?
Anything else you would suggest?