Well the basic philosophy is to make them logical. Large ships need a centrifuge section for the crew, fighters have a hull shape that minimizes the cross section when attacking, engines and weapons are modular attachments, every ship needs dozens of RCS thrusters… We have a lot of exposed radiators as well, because in the real world that would be a necessity. The ISS actually has a very large cooling surface as well, for example. We put solar arrays on small craft, nuclear reactors on largest ships…
Once you’ve got all these constraints, it’s really just a matter of designing a hull around all those components so that the ship makes sense.