In the episode, Thrawn learns that Anakin Skywalker was Ahsoka Tano’s master. This news appears to spark some emotion from the otherwise even-tempered villain.
In Timothy Zahn’s 2018 multiple-story novel, “Thrawn: Alliances,” one arc has Thrawn working with Anakin in the Clone Wars while another sees him with Darth Vader during “Rebels.”
It’s never explicitly said Thrawn deduced Darth Vader’s true identity, but several hints in “Alliances” make it clear he knew who the Sith lord was under the mask and suit.