I also have the interface/addons directory symlinked, the updates are much easier that way, and also the addons enabled and disabled information is stored in the WTF folder which i leave seperate, so I can just disable the complex unnecessary addons for the accounts running from my followers directory without affecting the settings for accounts running from the main directory.

I have never noticed any default loading addons that have caused any trouble or gone back to enabled after updating when they are disabled. What types of addons are you seeing loading without giving an option to disable on the character select page?

I think the overrides for which addons are loading should be in the
"World of Warcraft\WTF\Account\ACCOUNTNAME\REALMNAME\CHARACT ERNAME\AddOns.txt" files,
and should not be altered by updating an addon folder in a symlinked interfaces directory.

Though this may require you to check the box for just changing the addons selection for this character to create the localized addons.txt file.