In most cases, cooking actually increases the digestibility of the diet, making it easier to process and more importantly, releasing some of the available nutrients, especially when it comes to things like proteins and carbohydrates. The losses of vitamins, a typical concern, is relatively negligible, and of the nutrient blend that has been added in helps to account for any small losses that might occur or any batch to batch variation in those nutrients.
Cooking has the additional advantage of really being able to decrease the bacterial loads within the diet so that we can share that to some other diets where you may have higher loads of bacteria. If your animal were to become sick and you not know it, or have a compromised immune system, those increased amounts of bacteria could be pretty harmful and could even cause disease, and that is the last the last thing that we want, so the careful cooking process is designed to increase the availability of those nutrients and provide really the best nutrition that we can offer.
