Spaceship Design: What makes sense, and what's nonsense?

[thrash]

A lot depends on your tech assumptions. If you don't have force field reinforcement on your structure ("inertial damping fields") or other applied phlebotium, you should check that your design would make sense if you stood it on its engines (since that is effectively what happens when you accelerate). Don't forget that cargo (including munitions) and fuel/reaction mass will vary a lot over time, so those have to balance around the center line.

Likewise, no one ever gets required radiator area even vaguely correct, because it looks terrible and would be lethally fragile in a fight. (Discovery, from 2001, was as long and skinny as it was because it was supposed to have realistic radiator fins all along its length. It looked dumb, however, so they were deleted.)

Finally, remember: form follows function. Freighters prioritize cargo space; warships emphasize weapon systems. Neither one puts a premium on comfortable quarters for the crew. Any ship with a balance of all three is questionable, unless it really is a rich person's privately owned, purpose-built yacht-and-pirate-hunter. Choose the role for each class and optimize for it.