The engines that you can shoot (the ones actually located, subsystem-wise, next to the engine exhausts) are not really engines, but dummies. They are named something like "Main Engine, etc, which means that the game will not actually treat them as engines. The "fake" engines are the real thing, located at the center of the engines but inside the hull, with the glowpoints and engine wash values attached. My guess as to their presence is to fake a large engine subsystem without throwing out a rediculously huge engine wash, or as aldo said, a stupidly huge target for disabling.
