Nope, the parental controls only stop the user from launching internet browser, accessing eShop and launching online modules from games.you can block the wifi acess at all with parental controll, right?
If you are near a nintendo zone like hotspot (worst case ever because it only requires that the 3DS is with it's wifi on) or access point that was setup on your 3DS but isn't using tubehax DNS or other controlled environment the console will auto download the update and then nag the user until you do the cleaning routine explained by @Sliter