Not only that external processes would need that. I would ALWAYS recommand closing the game client before updating addons. And do not let Minion update automatically during game play.
Reason: If txt file chanages and need other/new dependencies the game client will not properly notice this and build the correct load order of the addons in all cases.
As this does not happen that often you might not get into the problems that are created by this very often but you could and thus auto updating addons in the background and updating manuallyif logged in/Playing is no good idea imo.
You are always safer if you logout at least.
But logout alone will not update the dependencies and txt files read properly. This will only happen if you close the game (not the luancher, I'm speaking of the eso64.exe) executable and restart it.