Because so many horses are hauled every day, I am going to talk about disease conditions related to transporting horses. Horses evolved to spend long periods grazing with their heads to the ground and yet we place them in trailers and tie their heads up for hours. Elevating horses' heads causes bacterial flora that are normal inhabitants of the upper respiratory tract to enter the lower tract. When horses cannot drop their heads, the normal clearance systems are unable to fight against gravity to clear these bacteria from the lower airways and lungs. This is the reason many horses hauled long distances arrive at their destination with pneumonia.
The veterinarians at Royal Veterinary College in Britain indicate that horses hauled for 24 hours required 8 hours to clear the respiratory tract. Stopping for rest for 30 minutes every 6 hours is not helpful. Also, restraining the horses heads has been shown to compromise their ability to balance in a moving trailer, and cross tying does not stabilize them but actually decreases their stability and it increases stress.
Colic is the other major concern with hauling horses as horses hauled one to six times a year have a higher risk of colic. However, those hauled over six times a year have a reduced risk as they are more comfortable with hauling and are less stressed. Sweating and failure to drink are the main causes of dehydration in transported horses. Dehydration directly decreases intestinal function and can predispose horses to colic. You can add flavoring to the water at home and then flavor the water on the road to hopefully keep the taste the same. A product called Thirst Quencher can also be added to the water and seems to help encourage drinking.