When the controller says heading, he means heading.
So if he wants you to go into a specific direction, he will take wind into account. The reason for issuing heading are:
- Every aircraft can fly it, because a compass is fitted on every aircraft. Track keeping requires more sophisticated avionics.
- If two aircraft fly adjacent to each other, the wind will offset them by the same amount and therefore separation is assured.
Quite often a controller will ask you to report your present heading prior to instructing a one so he can make more accurate adjustments to your course, especially if you were under own navigation before being vectored.
With Mode S radars and the right equipment in the aircraft, the current heading can be downloaded from the avionics without the pilot being aware of it.