I've also 'thumped' and clapping has usually worked too as it startles them out of their naughtiness!
I use a big piece of fleece (pet fleeces are really cheap especially from somewhere like Wilkinsons) for Hollie to dig in. They live outside in a shed plus aviary but they still need something to dig at lol. The fleece is shredded and full of holes - it obviously works at being something safe they enjoy trashing.
Clear carpet protector (the stuff with 'studs' on one side) might be a good solution to digging by the way - very cheap!
Also - not sure I agree rabbits need to get used to being picked up. It goes against all their instincts and I don't force mine to enjoy being picked up because I don't see why I should! So no, Scooter might not ever enjoy being picked up. I think rabbits that enjoy being picked up are the exception rather than the rule. I use treats if I need to get them to go back in their aviary etc....
..... works for my greedy pair!