Yes, deadly Aim can be applied to mystic bolt. It is a standard ranged attack that deals hitpoint damage. It even explicitly says in the rules text for the ability that you can take feats that apply to weapons - including two-handed fighting.
Piercing Bolts seems to be optional, so you are not forced to make the attack a touch attack if don't want to. If you are attacking standard AC and doing hit point damage then you can use deadly aim.