I don't have Pencil to test this, but the people who have Pencil and 9.3 beta have repeatedly said that the only thing that doesn't work any longer is scrolling with the Pencil. From that, I assume that pulling down Notification Center and pulling up Control Center and sliding in the multi tasking screen with the Pencil should all still work.
I don't think pulling in NC or CC or Slideover/Split Screen ever worked with the Pencil. (At least never did on mine in either 9.2, 9.2.1 and 9.3)