My main character is a sneak archer, and my latest one is a pure mage. While I can justify an increase in damage on sneak archery, I just can't see it for sneak spellcasting. With sneak archery, I look at it as though the baddies are leaving themselves more exposed (their vital spots are more easily reached when they don't have their guard up, that is). Magic is a completely different type of attack - it doesn't matter where you hit them, as long as you hit them. That alone doesn't justify a sneak bonus, IMO.
If an arrow did different damage depending on where it hit you wouldn't be able to one shot kill with an arrow in the arm or leg so your argument is invalid on that score. It doesn't matter where you hit them with an arrow either as far as this game goes, but Archers still get a stealth bonus where magic users don't.
With stealth, you have more time to make a proper aim and therefore do more damage. This is the theory behind the stealth bonus.
Put magic aside for the moment and consider ice bolt for what it really is: A pointed icicle travelling at high speed. If I hit you in the leg with it, it would do quite a lot of damage and hurt like hell but it would be unlikely to kill you. If I hit you in the face or full in the chest, It would be unlikely that you'd survive.
So in reality, what is the difference between an ice bolt and an arrow?
Fire bolt = Pointed stick on fire.
Shock bolt = Pointed Tesla coil.
Ergo, why shouldn't these have a bonus for stealth? They can still be aimed at more vital spots in stealth than they could if the enemy was aware and able to dodge.