Skin diseases are divided up into itching and non-itching types, so I really need more information. If he is itching, the most common cause of the hair loss you describe is flea allergy dermatitis. You do not always see the fleas, and some dogs are so sensitive that it only takes a single bite to cause the hair loss. If he is on good flea control, and you are sure there is not a problem with fleas, the second most common problem is allergies. If it is seasonal, it is most likely an allergy to pollens. If he is an inside dog, it can occur year round, since he can be allergic to house dust mites.
If the problem is not seasonal, then there is a possibility that he is allergic to some protein component of his food. To find this out for sure he has to be on a STRICT exclusion diet for at least two months. During this time he is to eat only one protein source, and cannot get commercial dog treats or any table scraps or leftovers. Many people will allow their dog to get into something unknown during the test and then declare that the test did not work.
If your dog is not itching at all, then the hypothyroid test should be repeated. Make sure that the TSH is measured too.
If nothing else comes up, I would suggest that you consult with a dermatologist at a local referral hospital or veterinary college.