Neutering will not stop him from scratching at the door.
Crating a dog is not bad. Canines are den animals by nature, so they enjoy a smaller enclosed area to themselves. If your puppy has separation anxiety, which sounds like he does, he will probably hate being crated at first. Don't use the crate as punishment, but you need to lock him up if he is going to destroy your house.
You need to start training him. Random snapping at people should never be allowed or tolerated.
Usually the scrotum is cut open and the testicles are removed through the opening.
Here are some fun pictures of the procedure if you're interested: