Uh, I think the anime is to blame for the color changing. A pure white cat with blue eyes will very likely be deaf — one blue eye means that side is deaf. The manga has Luna with blue eyes in feline form, Artemis did not have a human form in the anime and in the manga his eyes are green as a feline.
In the manga Luna's eyes are always blue and Artemis' eyes are always green. We never see Artemis or Diana as a human in the anime, but for whatever reason they decided to keep Luna's eyes blue in her human form in the S movie. Probably because it does look a lot nicer.