Eyes don't matter... unless they do! Guide flies are not all created equal and sometimes incorporate eyes and the like, but they generally are fairly minimal. Just what is necessary to get the fish to go.
Fish in crystal clear water (particularly saltwater, in my limited experience) can be very picky, and that little extra bit of convincing an eye/gill/etc. provides can make the difference between a follow and an eat, especially with slower presentations like shrimp. Of course, when fish are actively feeding on small baitfish, they don't spend much time looking at induviduals before they strike. In those (glorious) situations, eyes probably make little to no difference.
I usually use "eyes" (often the weghted variety) for functional purposes more than attraction, but that doesn't mean I don't try to use the most convincing size/color. As has been mentioned, holographic eyes (besides looking really cool) create a good foundation for creating UV bodies on baitfsh patterns. Yes, they look cool to us, but eyes can serve many legitimate purposes and can quickly turn into yet another fly tying rabbit hole.