Lucas never went into the specifics about why this scene was cut but it is Shaak Ti's canonical demise as confirmed by Star Wars: Galactic Atlas, written by Emil Fortune and illustrated by Tim McDonagh, and published in 2016. The scene does eventually appear on screen in two different properties. RELATED: Why Star Wars’ Deadliest Lightsabers Were Dishonorable to Jedi - and Way Too Dangerous Mildly irritated, she asks, 'What is it, Skywalker?' and before the next breath, Anakin kills her in silence. Another blade goes through her back, boring a smoldering hole through her sternum, and Anakin leaves to saunter through the carnage he has wrought. She remains calm because she knows him well and has not sensed his intent. While her eyes are still closed, she is aware of the intrusion as well as the identity of the intruder.
Another deleted scene from Revenge of the Sith shows Shaak Ti meditating in her quarters when someone enters.