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Gabriel Cousen's book "Conscious Eating" has a chapter on enzymes. Under the heading "Importance of Preserving Enzymes", he discusses Dr. Howell's findings and other research. He cites a study on dogs who were switched from a raw food to cooked food diet. After one week, the enzyme content in their saliva was greatly increased. The conclusion he makes is that the body only secretes the amount of enzymes it needs to digest the food.
Since the dogs' bodies had to secrete more enzymes to digest the cooked foods, this is evidence that the body is able to use the enzymes in uncooked foods in some way. Whether that be in pre-digestion, the stomach, or later on in the intestines (some suggest that stomach PH levels deactivate the enzymes, which are later re-activated in the intestines.)
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