Hisui definitely knows he's an invader; that was established in a brief flashback when we saw she was actually lucid when he fought that one guy who was brainwashing her. She seems to be genuinely attached to him, too, so the stare you mentioned was actually her being concerned. So far, it seems that Green Keeper AKA Chidori isn't telling her that he knows too though (and probably knows more than her, since she should't know D has been trying to hunt Keepers), or at least that's my impression.
As for Usukubo, well, if there wasn't something up with her then there wouldn't be this much foreshadowing and foundational character development spent on her. Her full name is even Usukubo Enjeru/Angel which seems kinda... unique. But I doubt she's literally a foot soldier like him. I kind of waffle between her and Suzukiri as the possible candidates for a theoretical invader-human hybrid or some similar dramatic plot device... (But maybe my mentality toward heterochromia was just warped because I read Tokyo Ghoul.)
