Android - 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.

If you don't use them, there is no point in updating them.

The only benefit of updating would be that they will stop giving annoying reminders to update - at least until their next update. Many of these bloatware/crapware additions can't be removed without rooting the phone. However, many of them will respond to a Force Stop after which they won't prompt you to update until you reboot your phone. The really annoying ones are those that restart after a Force Stop.

Most updates increase the amount of memory used by the app. Leave them alone if you don't want them.

In terms of security updates, if the app isn't running then it isn't a risk.