If a character in The Host ever said "the eyes are a window to the soul" they would be right—in the most literal sense.
On Earth, Wanda's species call themselves souls. How do you know if a human host is occupied by a soul? By a faint silver ring in their eye, like a really pretty case of eye-ringworm. Therefore, the eyes are a window into seeing the alien souls.
But the eyes are also a way to see a person's true intentions. In the caves, people often glower at Wanda, "regarding her with hostile eye." (20.46). In fact, the humans' anger almost makes us long for the gentle souls residing behind silver eyes. A person's true nature is revealed in their eyes., and it's not always a pretty sight.