Euphy worries about Suzaku, though she isn't sure how, or if, she should bring her worries up to him. She knows that he's very important to her, but at the same time he's almost like a stranger to her. So it makes it hard for her to go, "I'm worried about how the darkness affected you," since she has a feeling that Suzaku would brush off that concern and turn it back to his concern for her somehow.

Probably the one that's most helped her impression of Suzaku along, and confirmed her worries, was Lelouch. Even though she's certain that both he and Suzaku are hiding something big from her, neither has much motivation to hide when something's wrong with the other. Lelouch told her about the darkness, and it's from that that she realized that even if his responsibility is to protect her... It's her responsibility to care for him.

And while she believes Suzaku is telling the truth, she also thinks that wasn't the whole truth of why Lelouch is acting strangely, but it's another hunch that she has no reasonable ground to call him out on. So, instead of being frank and open, for the moment she's decided she'll work with a more subtle approach to both Lelouch and Suzaku.

What are Suzaku's main worries for Euphy in Aather?