I've always built my ships in a cube shape, for one simple reason.
Cube-shaped ships are easier to edit, in particular, easier to upgrade.
If I want to attach, say, a hangar to one of the ships I see on the steam workshop, I might as well scrap the ship and use a different one.
But with a cube-shaped ship, its perfectly doable. Cube-shaped ships are modular, you can easily swap out bits, upgrade things, etc.
That is THE reason I use cube ships.
Not any of this stuff about surface-area-to-volume ratio, or armor plat HP, or similar.
Simple ease of editing.
If you want to discourage cube-shaped ships, then you need to make it easier to edit/refit/upgrade ships.
Start out by giving us better control of the editing camera. Editing something inside my ship should not be so hard.
Alternatively, forget about the idea of making ships pretty. Avorion is a primarily single-player game. Even in multiplayer, the universe is vast, and I will never see most other players' ship.
How ships look doesn't really matter. Practical concerns are vastly more important. We're building warships here, not luxury liners.