I thought about it for a minute because I agree that Yen's purple eyes look much better than Ciri's and Geralt's lenses, so initially I thought you made a good point. But then I thought back about the Star Wars prequels that came out between 1999 and 2005, and how the 'Sith eyes' in those were made using bright red and yellow lenses. I never had a problem with them, in fact they look good to me. My problem with the lenses in the Witcher has nothing to do with colour and everything to do with the fact that the two actors have that dead-fish look about them when they're filmed in close up. I wonder if it's because they found it difficult to get used to them and rarely ever blink, or if the lenses moved about a little and gave the illusion that the characters were cross-eyed . In the scene between Geralt/Dandelion and the elves of the second episode, Cavill made me think of a chameleon simultaneously tracking flies on both sides of his face.
But the 'Sith eyes' example points to what I was saying earlier. How many contradicting expressions you could expect from a Sith Lord? A Sith Lord cannot show anticipation, compassion, love, annoyance, frustration and lust under a minute in his eyes during a conversation, he is not expected to have those conversations either. Also, all Sith Lords have some sort of a concealing, heavy make up complimenting to their eyes. It's either covering all their faces, around their eyes or something strongly emphasised to make them look distinctively inhumane and evil.
Witchers look like humans. Peoples of the realm are scared of witchers, they believe as the result of the trials, they lack human emotions and so they lack conscience; a kind of human morality. And considering even the trained, armed military is often helpless against a witcher while often everyone needs them, they have a point. It's a cat-canary situation. But besides these obvious reasons, what is the first physical thing creeps them out? His eyes. It's the only nonhuman trait that can be seen from outside. It's like a confirmation of his 'inhumaneness'. So the expressions in the eyes gain more importance.
While Geralt has a human makeup and yellow eyes, he is supposed to be showing all range of emotions when needed; he sees, feels too much. (Siths don't need that. The whole point of being a Sith is that you don't need/have to have an excuse, emotion for anything. That's why it is so 'in' in the 21st century and even used as a synonym for real human conditions. Do you know anyone who wants to be a 'witcher'? No, because it is too blip blip hard and painful being a witcher.) And considering Geralt is a special witcher, he probably feels and shows more than any other, because the world
he lives in,
his range of experience -with nature and all kinds of races and classes of people-
his vision of life in that universe is far greater and richer than other beings; even other witchers, mages, sorcerers, warlocks or barbarians...etc. (Following the typical characteristics, there would be exceptions.)
So the colours and the colour match with emotions, expressions... the characters, the categories they are attached to in the human mind... big problem.
Why does Drizzt have lavender eyes while the red eyes is the characteristic trait of the drow? The colour lavender (or purple) is not even remotely alien in the dark world of Menzoberranzan. (As yellow or red is not in ours or in the Witcher's.) With their dark black skin, red eyes -or anything with a taint of red- the drow are very aesthetic and fitting in that world besides fitting a fundamentally dark race in the story. Lavender eyes with black skin? How alien Drizzt must look to his own kin with his expressions, let alone the surface dwellers. But Salvatore chose to give him different colour of eyes so he wouldn't fit in there and stick out like a sore thumb. Geralt is more 'humane' than any other race -also his own- and he sticks like a sore thumb because he is none of them. And if they make a series of the Dark Elf Trilogy, Drizzt's eyes will look more expressive than any yellow or red eyes. Because it will be an easier job for the makeup effect team and most importantly easier for us, real humans to read/match it that way.