I don't know the answer. But I was thinking, how can you figure that out? Here is how I would do it:
1) Go to an airport where magnetic declination is large (e.g. in South Africa, where it is around 30 degrees).
2) Move your aircraft next to the windsock.
3) While in the cockpit view (F9 in FSX) take note of the current magnetic heading of your aircraft (use the compass or the gyro).
4) Set the wind to blow from the same heading at 15 knots or more.
5) Switch to the outside view (F12 in FSX). Zoom in/out as needed, until you can see both the aircraft and the windsock.
6) Are the windsock and the aircraft parallel to each other? If yes, it means your simulator is simulating the winds using magnetic heading. If no, (i.e. if you see the windsock at a 30 degree angle to your aircraft) then it is using true headings for wind.
I really, really hope that all simulator use *true* heading.