Ship building is an art
As long as they are fast, do good damage, and are well armored I'm happy. I always uses my weapons and engines to line the outside of the ship to take all that directional damage first.
I also make a point of checking the HP of each outer subsystem, comparing it to the hull health, doing some math with regards to the hull aborption % to see how much overall damage I'll have taken by the time they've broken through to my inner components, and using bulkheads as necessary to bring 'death of nonessential components' and 'death of ship' as close together as possible. Heavy hulls are nice since they often don't require bulkheads at all. Some ships don't get min/maxed in this way, such as fighters or super heavily armored ships and nano armor focused ships.
But, my favorite type of ship is the carrier. Not in this game specifically, but in general. I love carrier combat. Any game that does it well is an instant favorite.
So, my main ship is my supercarrier. I make mine scale 2500. Got all the normal trimmings of any good carrier. Loaded down with plate, powered, and nano armor. It uses light hull and the internal components arent bulkheaded though, so it relies on sheer scale and armor to survive. I also have a small construction bay, solely for the ability to construct a single colonizer after clearing out an enemy system. Refill materials at the new planet, jump to new system, repeat
no need to manage the movement of colonizers in tandem with the carrier to catch planets before someone else.
It's filled with size 5 heavy fighters. Those things are monsters. 2x size 2 railguns with 1.5 coolant systems on both. They are heavily armored and can generally take quite a few hits from ships up to size 100. Probably the most exciting moment in the game for me was when I figured out reactive armor, and realized I could make massive swarms of deadly fighters that are also tough as nails even for significantly larger ships.