I'm on auto-update (for the iAVS, anyway), and I get the pop-up notification afterwards. I've turned sounds off since I don't have speakers and only use the headphones for some games.
I might be wrong, but I think turning the notification on/off would have to be done by playing with the ini file, rather than as a setup option. Technical did a marvelous thread on the ini here somewhere, and I'm sure quite a few of us have that link bookmarked and will be happy to stick it here.