I would imagine that they are not shorted to the frame in most cases. Your windows don't only roll one direction do they? I've never seen a window motor that has some form of transmission that allows for switching directions. The leads would have to be isolated from the case, generally a car frame is grounded and this includes the doors and most metal panels attached to the car.
Edit: I haven't seen this, but I would imagine two sets of windings could be used inside the motor and both leads could be 'hot' and the case could be grounded, but this sounds more expensive than it is worth.