With those long hours, I can see why he lays on his waste. They aren't humans, so they don't necessarily think it's "dirty" to do so. He's gotten use to it, and clearly he has no problem with it, considering the small amount of space he has.
I use to keep Missy in her crate for some long hours and boy did I ever regret it, so I chose to keep her in a bigger area, where everything is basically 'baby' proof. You should definitely get a pen
