I’ve heard that Kubrick destroyed his deleted scenes. I’m not sure if that’s true though.
The 2001 trims were found in the salt mine MGM/Warners uses for a film vault a few years back. (My money is on them being included as an extra in a 50th anniversary video release next year.) The pie fight from Dr. Stangelove is also rumored to exist.
Unused footage from The Shining was allegedly burned, but the many hours of footage Vivian Kubrick shot for her making of documentary now reside in the Kubrick Archive in the UK, along with footage she shot for a never completed doc on Full Metal Jacket.