Maybe not the whole time, but…
There are some hints that she might have actually been aware that Varrick was behind the conspiracies.
One of the issues that Mako had as a rookie cop was constantly barging in on Lin with his evidence in public; she’s in a meeting with the president, “Chief! I think I know what’s up!” She’s interrogating the captain while Varrick is in the area…”Chief! I have important evidence to present to you!”
Procedures exist for a reason.
And Lin’s not stupid. When Mako started spouting about how he was “set up,” I think Lin immediately went, “Okay. Something’s wrong here.” But unlike Mako, she knew not to play her hand and go around parading the evidence; she had Mako locked up, but in the nice cell, and kept out of the way. If there was another attack, he couldn’t be the one responsible; if the person who framed him wanted to get to him, they would have to bust into the prison, so Mako’s safe; also, he can’t scare off the prey by loudly waving the alarm bell.
And the moment that Varrick was exposed, she was at the door arresting him. Either Lin can teleport, or she was already on her way to secure him. She had already sent men to protect the president, she didn’t go down to help Bolin with the thugs—she was already moving on Varrick. Mako had presented her with all of his theories and evidence…but she didn’t have a rat. She needed someone to point the finger before she went after him. After all, Raiko had established already that her job was in a shaky place—if she believed Mako’s hints and accused Varrick and he weaseled his way out of it, her career would be over. She would be disgraced, and she would have lost all of her progress. If Varrick was eventually exposed, she might be reinstated…but not if she was assassinated by thugs because she knew too much.
And when Varrick and Zhu Li were led off in the van, she was happily explaining everything to Raiko—and reminding him that Mako knew about everything. Not once does she show surprise in that episode. She keeps a level face, and has a proud smile when she’s talking to Mako.
Because I think Lin was just that skilled at the game.