Paco,
Sorry! No!
Do you have a headache? (Now, this time, not habitutal.)
Are you having one of your headaches? (Now, this time, not habitual.)
Do you have headaches? (habitual)
Do you get headaches? (habitual)
Have you got a headache? (Now, this time, not habitual.)
*Have you got headaches? (Impossible when speaking to one person, except for aliens with two or more heads!)
CJ