The question on health care coverage in the HSA interview refers only to the person who owns the HSA. I presume that this would be you, not your son.
Family coverage in an HDHP means that it covers you and at least one other person, even if that person is otherwise not qualified for an HSA (your son is disqualified from having his own because of the Medicaid). However, if he is your dependent, you can still use funds in your HSA to pay for his qualified medical expenses that were not already covered by any insurance (HDHP, Medicaid, whatever).
So in the normal course of events, you would not even mention that your son has Medicaid, if he doesn't have an HSA.
@Anonymous
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