You can buy pads and such to line the kennel so it absorbs liquid and smells. Most animals won't eliminate for several hours anyway, similar to leaving them home while you work and then letting them out to the yard when you get home. Additionally, when animals are nervous, they tend to avoid eliminating, eating, and drinking. Whenever I move my cats to a new home, they don't eat, drink, or use their litter for about 12 hours or more.
Since I hate doing that to them, I would never travel with them. The only time they're going to travel is when we move cross-country, and even then, we have a pretty good plan in place (finally) that will make it as easy and relaxing as possible for them.
I know dogs tend to be much better travelers, but I still wouldn't put them in a kennel in some kind of animal car for that long. That's just me, though. I'd rather take the dog in the car with me if it loves car rides (and I think most do).