When Kara Danvers (Melissa Benoist) became Supergirl, she spent a year working for Cat Grant (Calista Flockhart) as her assistant while hiding the secret of her dual identity from Ms. Grant. By the end of Supergirl season 2, Cat revealed she knew Kara's secret all along, which put her mentoring of both Kara and Supergirl in a new light. With Ms. Grant now serving as the Press Secretary for the President of the United States Olivia Marsden (Lynda Carter) and James Olsen (Mehcad Brooks) running CatCo, Kara at least thought her days of hiding her dual identity from her boss were over. Until her best friend Lena Luthor (Katie McGrath) bought CatCo and became Kara's new boss. As Kara put it, this is "a new kind of horrible."
Not that Lena herself is a horrible person. Since she was introduced at the beginning of season 2, Lena has easily been the nicest person in Supergirl with the surname Luthor, and that's counting her incarcerated and yet-unseen half-brother Lex. When Lena arrived in National City as the new CEO of LuthorCorp, she promptly renamed the company L-Corp to help distance it from Lex's criminal legacy, as well as Cadmus, the alien hunting underground network run by her mother Lillian Luthor (Brenda Strong). Lena bonded with Kara over the course of season 2 and in the season 3 premiere, when Morgan Edge (Adrian Pasdar), another villainous billionaire mogul, threatened to buy CatCo and turn it into his personal tabloid, Lena bought CatCo from under him, partly because her best friend Kara was a reporter there.
However, Lena remains the only person in National City with a close relationship to Kara Danvers who doesn't know Kara is Supergirl. Or does she?
According to Supergirl's Executive Producer Andrew Kreisberg when season 2 wrapped last summer, Lena doesn't know Kara is Supergirl. This was also evidenced during the climactic crisis involving the Daxamites when Lena and Lillian worked together with Supergirl, Mon-El (Chris Wood) and the DEO to help stop the invasion. At one point, Queen Rhea (Teri Hatcher), who duped Lena and pretended to be her mentor, tried to force Lena to marry her son, Mon-El. Lena learned that Mon-El was dating Kara Danvers. Later, Lena asked Supergirl if she was aware Mon-El was dating Kara; Lena even missed the knowing glance Supergirl shared with Lillian, who does know Kara's secret identity, having worked with Kara's adoptive human father Jeremiah Danvers (Dean Cain) in Cadmus.
So far in season 3, Kara hasn't done a terrific job hiding her suspicious behavior from her new boss Lena. Kara has spent the months since Mon-El was forced to leave Earth after the Daxamite invasion was foiled mourning the loss of Mon-El and wallowing in her own guilt and anger. Kara spends most of her energy fighting crime as Supergirl with a rigid resolve while pushing her life as Kara Danvers - and her friends and family - aside. Kara's behavior is noticeable, not just at the DEO, but at CatCo, where Kara blows off Lena's assignments and keeps disappearing without explanation during work hours. Kara finally offered some form of confession that she is still hurt over Mon-El. Lena, who as a Luthor isn't used to having or being an actual friend and has been seeking genuine relationships in her life, forgave Kara both as a boss and as her friend.
However, it's hard to believe Lena doesn't at least suspect Kara is Supergirl. Cat Grant figured it out, and despite the cousins from the House of El's insistence that glasses are enough to hide their secret identities, only a fool couldn't see the blatant resemblance between Kara Danvers and Supergirl. Lena has made mistakes trusting people, like Rhea and her mother, but she's no fool. Lena has also spent a lot of time with Supergirl as well as Kara. The only explanation for how she wouldn't have put two and two together when it's literally right in front of her face is because she hasn't wanted to see the perfectly obvious. Or she really does know and she just isn't letting on.
Lena may not be the mad genius Lex is, but Lena is a gifted programmer, runs two corporations, and is herself highly intelligent. It's very hard to justify how Lena doesn't know Kara is Supergirl, when all of the evidence in the world points to them being one and the same. But let's say somehow Lena just hasn't figured it out for whatever reason. She eventually will, not just because secret identities are nearly impossible to maintain in the Arrowverse, but because Lena is no fool.
When Lena will discover the truth is the question, but it most likely won't be until Mon-El makes his return to National City, under whatever circumstances that will be. The change in both Kara and Supergirl's demeanor when Mon-El comes back will be evident. What's more with Lena having turned over day to day operations of L-Corp to Samantha Arias (Odette Anabelle) so she can spend all her time at CatCo, Kara's inevitable frequent disappearances will be impossible to miss and explain away forever, even with James Olsen covering for her.
Or maybe Eve Teschmacher (Andrea Brooks) will find out about Kara and tell Ms. Luthor, in a fun spin of Lex Luthor (Gene Hackman) and Miss Teschmacher (Valerie Perrine) in Superman: The Movie, which would be an homage very much in keeping with how Supergirl honors Superman lore. When Lena does find out, however, she could treat it as a betrayal that could spark Lena's journey towards a more villainous path. Evil, after all, is the real Luthor family business.