The Enterprise is a distinct saucer and cylinders shape - why?
I used to think the saucer had to do with warp field geometry. That is, in-universe. In the real world, probably just because saucer = spacemen. And that the secondary hull was separate to be detachable, of course, but also due to the space requirements of the deflector array - a part of the ship integral to warp travel, and necessarily just that big in relation to the rest of the ship, for it to reach those speeds. Also, I thought the nacelles were apart (unlike the Saber and Steamrunner Classes) because they were hazardous in some way.
But none of that seems to fit all the different forms of ships we've seen. Alien ships you can discount to a degree because aliens will think of alien ways to do things, but it seems like most of them also don't follow my guesses as the why the Enterprise looks the way it does.
And if it doesn't need to look that way, it's a pretty silly, if intriguing, way to design a ship.