Should I update those pre-installed programs that I never use?
You might consider disabling those apps (starting with ICS, that's possible for some but not all) and "delete their updates". This way you'd solve multiple of your issues:


no more update reminders
app becomes unavailable, so it's no longer shown in the app drawer
being disabled, they should also no longer provide an "attack vector"
plus, the updates deleted, you save precious internal storage :)


If that's not possible for some apps via Settings → Applications (check the "All" tab there to see pre-installed apps), and rooting is an option, you can still freeze them with apps like Titanium Backup to achieve the same.

Update: Starting with Lollipop, you can use the pm hide command without root via adb. So in case disabling an app the common way (see previous paragraph) fails, that is still worth a try.