May I add though not to rule out anything until test are done.
I personally have had episodes where I wake up early in the morning with a low and after getting sugar in me I go back to bed. Then when I wake up for work or school I have an excruciating headache that I can't get to go away for the rest of the day. Some days I wouldn't call it a migraine, but there are others that have landed me in bed the rest of the day.
I have to agree with JDRF-VOL-RL that your son's headaches sound worse than those that can accompany hypoglycemia. But I did want to add that low glucose levels do often show themselves with headaches. So if your doctor has no other ideas, it probably doesn't hurt to perhaps get a blood glucose test done on him, ideally while he has one of his headaches. But I agree with JDRF-VOL-RL that these sound more like real migraines than hypo headaches. And, no, headaches are not a symptom of diabetes.
Hello. I'm not a medical professional, just the parent of a kid with diabetes. If your son has only the symtoms you describe, then hypoglycemia or diabetes are not the cause of his problems. The main reason is that Motrin is not an effective treatment for either condition. Migraines are not common with either condition, and if you aren't seeing any increased urination or thirst, or any of the other symptoms of hypoglycemia (http://www.childrenwithdiabetes.com/download/NovoHypoglycemia.pdf), then I'd say your son's problems lie elsewhere. Good luck.