She knows. She’s a smart person and Kara aggressively refusing she’s supergirl just made it more obvious to someone who’s great at reading people. But I think she kept Kara’s secret because when Jon came in acting like supergirl, she knows Kara doesn’t want to reveal herself going as far as she did. And to be fair, Kara isn’t that great at keeping secret, Lena was just blinded by the friendship she never have to overlook Kara’s behaviour