I watched the both episodes and I kept wondering why she had pupils and her army does not. am I missing something here? :|
Don't rulers look different from armies? Anyways, I think its because of her snake like features. (fangs, eyes, etc.)
To make her eyes more expressive. She was such a major character that blank eyes would have been impractical, especially in a show that relies so heavily on facial expressions to convey emotion.
They didn't need to be expressive. If anything, an army of expressionless drones is even more intimidating.
I could totally agree with the eyes as a form of needed expression, but I am going to go with drones not having the full features of the queen. Simply out of the physiology of the species. OR She could have easily just been using the same illusionary magic we saw in the fight between the mane 6 clones. The drones might not be physiologically handicapped, but simply being respectful of their queen.