If we're going to talk about ships missing from the wall displays in TMP and TNG then you have to mention the most famous real Enterprise. The World War 2 era USS Enterprise CV-6; the most decorated US warship of the war. Which was cut up and sold for scrap.
As for the ship design of the twin nacelles and saucer. I always thought that the design was a result of the warp field geometry of a flattened elipse.