"Is your head still aching" might be closer to the structure of the Czech original.
Edit: By “closer to the [Czech] original” I meant that
- the subject (hlava) remains the subject (head)
- the verb (bolí) remains the verb (is aching)
Both are not the case in “Do you still have a headache?” where both the subject and the verb are condensed into the noun “headache,” while “you have” becomes the new subject/predicate.