Ironically, the ship design helps against that.
The very long and huge cargo block the bulk of the ships HP, and because of the framework, I use many small thrusters spaced out, something to the size of 0.5 x 1.0 x 1.0 (Spread out, they're incredibly efficient.)
The occasional shots will only take out some framework and a few of the thrusters, which are quite cheap to repair. (Iron and titanium in trinium territory if you can believe it)
This is the starting model; later on I scale up once, and afterwards copy the whole thing without the engines then paste it to the front (or bottom/top/sides)
Sorry about the colors, but everyone's ships are such ... somber death machines, all that black and red, really boring.