I love shipping boots. And I cant understand how they did the damage you are claiming they did, unless they were put on way to tight, or the horse was standing in the trailer, not being able to move, for a long period of time ( for trips longer than 2 hrs the horse should be removed from the trailer and allowed to walk).
I personally think bandaging is more of a risk, because it can create uneven pressure (leading to bows and swelling), can unwrap and become tangled around legs, and you shouldnt need to rely on something for support anyway, if the horse is allowed out to move and get blood flowing again. Rubber matts and sawdust also make for a much softer surface for the horse to stand on, if you are concerned about the horses legs.
I was always told never to bandage over a horses joint, as it restricts movement.
Bandaging is something that needs to be taught properly before attempting it. Far to many people just go out and buy bandages and slap them on, having no real idea of what they are doing, or even why!