Deadly Aim gives me 3x damage when using bow while Sneaked. Does this apply to damage in general, or does it also apply to effects? For example, I'm using a bow which does 22 damage, and has been enchanted to do an additional 10 shock damage, with 5 damage to Magika. So do I do 66 damage, with 10/5 shock damage, or 66 with 30/15?

It would just times the 22 by 3. So yeah 66, the 10 shock is just bonus damage to whatever damage you hit it with and the magicka damage stays 5.

Only the base damage of the bow and arrow combined.
Any damage from enchantments is applied after the x3 multiplier.