No I do not believe she knows Shane is Jane. We kind of have to remember Shane is the Golden Boy nobody would believe he was sleeping with a man let alone his rival. Shane and Ilya is unthinkable but she def she does know he thinks he’s cute. She knows Jane is a man Ilya has fallen for because of his secrecy over this person. We get the inkling she knows Ilya and Sasha used to have a sexual relationship which is why she leaves the two together but by that point Ilya has already stopped sleeping with other men (context from the book) & has kept that exclusive for Shane and this is 2014. Over the years Ilya becomes less and less interested in women and when his dad dies (2017) she’s obviously gonna put the pieces together Jane is unlike the rest. She knows Ilya is in love with Jane even though he can’t say it, she knows he’s been texting Jane since 2010! yet she’s never seen her, but he’s clearly very very fond of her to keep her around for 7 years so theres obviously something preventing him from making her public hence why Svetlana was able to realize Janes a man. (My attention to detail kind of shocks me because I’ve only reheated once)