If the nerves inside the eye like the ciliary nerves get damaged could it effect the color of the iris resulting in a darker colored iris?

Color: Ciliary nerve damage probably will not affect eye color. Damage to the eye from trauma, might cause eye color to get lighter, not darker. Certain eye medications, such as latanoprost, may cause eye color to become darker.

No: Only congenital damage to the nerves can change the color of the eye. And it is usually lighter and not darker with a ptosis ( cong. Horner syndrome.) in adults damage to long ciliary nerves results in smaller pupil and a slightly droopy eyelid on that side, also horner syndrome which could be sign of lung cancer especially in smokers.