I think it does make a difference. Many do; a fair number do not.
If trying to imitate a particular prey, I will use the eye color of that prey surrounded by a little contrasting color on the head. If not a particular imitation; I usually will do one of two things. Either the eye color of the predominate food source for the fish targeted, or a contrasting eye versus the "head color" that the eye is applied to ( either the bait or jig head ). Prey try to camouflage their eye's from the predators. I try to emphasize the eye. This is for most fresh water fish. Salt water in clear open water it's match the prey all the way. Inshore, it can go either way.