If we actually want to discourage cube ships, there are plenty of options.
1. Make local damage not respect block size. A 1 meter thick armor plate that's 100 square kilometers in area is just as easy to penetrate as a 1 meter thick armor plate that's 10 square meters in area. Let blocks be partially disabled by concentrated fire.
2. Require (or at least strongly reward) some blocks to be distant from the center of mass of the ship. Thrusters are too effective when close to center of mass if we don't want cube ships. If a cube ship, even with all of its outer layers composed entirely of thrusters, had rotten turn radius, and instead required long pylons to give the thrusters leverage to turn its massive bulk, that would discourage tightly compacted ships, especially cubes.
3. Have components generate heat, and have to radiate it out to space. Yes, you'd end up with cubes covered with spikes, until local damage shoots off enough of the spikes to let the ship's waste heat cook its crew.
I don't know that any of these options are good ones, but they all would have some effect to reduce the relative power of cubes vs. everything else. As long as compact structure, small surface area, and large solid blocks are favored, cubes will dominate.