My position is that the update-notifier is for people who are mainly concerned that Linux should be "just like windows." It'll never see the light of day on any system that I use or assist in maintaining.
Once a week, or so, ...
# aptitude update
# aptitude full-upgrade
... will keep you current.
If you've been using the obsolete apt-get, you should run "# aptitude keep-all" once before converting to aptitude.
If you use Gnome, I suppose you could activate the update-notifier using the gnome-applets GUI app.