Do doctors still use VQ scans?

Yes. Still used to evaluate for pulmonary emboli in patients that can't have cta of pulmonary arteries. Can be used to evaluate patient for surgery. See radiologyinfo.Org.
Yes. Vq scans are still performed but not available 24 hours / 7 days per week in all institutions. Vq is often performed if there is a contraindication to ct scan such as increased creatinine level. Vq scans are also used sometimes in pregnant females to decrease radiation dose.