Let's entertain the idea of: What if Lena Luther found out very early on that Lena is in fact Supergirl, since she seemingly had no issue finding out about some other peoples real identiys why not this too.
But Lena being Lena does not tell anyone that she knows espcialy not Kara, she does not act like she knows since she is a Luther she can do that much since it's not her place to say that she knows about the truth.
Instead she waits just to see when Kara and the others will finally tell her, when she finally gained their trust of knowing. This way years go by and she really tries not to be hurt by the endless lies, by the fact that other people get told but never her. Never Lena who knows her seemingly best friend by then since years.
Now when she finally do snaps she is even more hurt then anything else, by the fact that they do not see as to why it hurts her so much.
This lie never was meant to protect Lena, okay maybe in the beginning but after that? after years? years of Lena being in danger constantly anyways, years of their other friends also joining in on the lie over and over again.
And she is supposed to act like it never happend in the first place, to act like she will just continue to help them for other peoples sakes?
But what if she does not? what if she stops and due to knowing Karas real identity since forever she does not go silly rogue for a bit, no. Inatead Lena just stops caring, she stops giving their friendship her 120%.
She starts to prioritize herself, to take her distance to be "selfish" as well.
She takes her time to truely Life again without truely knowing where she stands with people she thougth of as friends, she does not let herslf be sweet talked back.
She will take her time all the time she needs even and if she comes back then with more boundries with rules and conditions, she is not one for endless second chances.