I am having the same issue. Apple support could only tell me what I’d already done, which is unpair and repair the pencil, uninstall the game (Thereby losing all my worlds!!! Thanx heaps Apple!) Pencil works everywhere else but MC, following MC update.
I am using Ipad pro, 5th generation and Apple pencil 2. Pencil ONLY doesn’t work in MC after update. I use MC - the original version.