No the games still want to update because your 200+ slots aren't stubs if you have an cios installed. ( unless you have your cios double patched )And it will enable you to play retail games without your system nagging for an update.
Also it can prevent online updates.
There is a safer way to do that, which is to update to the latest version.
Installing themes or wads shouldn't be done by anyone that doesn't know what they are doing, because of user error (which you already said priiloader doesn't prevent).
System menu has nothing to do with that update.
Also when nintendo updates ANY ios, you can't update without getting some kind of hassle. I'ts nice to have priiloader in those cases as it will circumvent those updates.