Yes i think the glass is devided into two objects, the outside glass (which should be in the glass folder) and the glass viewed from the cockpit (inside).
So the outside scratches are in the red channel of the GLASS_DetailMap01_mask.png file. You just need to paint the red channel black.
The green channel is for the icing effect as far as I remember and the blue channel is the finger prints.
here is a picture from the SDK:
The inside cockpit glass is the other texture.
If you dont want any glass at all you need to change the GLASS_DetailMap02_mask and make it 100% transparent.