I also would drive straight through. We normally trailer 3+ hours to shows sometimes and we don't stop at all. I think stopping, unloading, loading a lot can put unneccesary stress on the horse, especially if they're a bad loader. Just leave them in the trailer where they are content with a hay net :)
And I only use boots if there is more than one horse on the trailer. Unless your horse is a stall/trailer kicker, you should be fine.