Interesting thread. I'm of the opinion that ones needs to analyze the anatomical features of the bait that one is tying. Eyes seem to be a prominent feature that predators key on, e.g. striped bass, that attack their prey from the front. A common bait on the flats is the sand eel. It has a yellow iris and black pupil. Other bait fish, as Juro mentioned. have white iris and black pupils. If you want to tie a fly to imitate a snapper blue for SBFT, it has a yellow iris and black pupil.
I tie my flies accordingly, but does it Matter? I don't know, but I feel more comfortable attempting to emulate the prey of choice. It doesn't stop there however; then it comes to the presentation, and strip/retrieve, which I believe, is more important.