Just for fun, I just tried a factory reset from within stock recovery (hold x on boot, when the exclamation point shows press the search button/magnifying glass on the keyboard, choose wipe data/factory reset and then when that's done choose wipe cache). It wiped and rebooted fine, when I got back into the os, the hidden apps were still gone, as was all my user data. A reboot put me into bootstrap (clockwork) recovery where I restored nandroid to get my data back (so a factory reset doesn't really touch the system partition, mostly just the data partition).
So as far as I could tell a factory reset does not add or remove anything from the system partition, it only wipes the data partition killing user installed apps and data. If a system app has been disabled or removed, it will still be gone after a factory reset. (This has been shown already with the droid 1 and other android phones)
A Nandroid restore (from within clockwork) on the other hand will put things back the way they were at the time the restore point was made.