Something strange is that the best armor is often a mess full of holes with plates linked to the build by a single little piece. This is obvioulsy to fight cannons: the less dense your armor is, the less parts will be hit.
That lead to builds that are both horrible looking and totally unrealistic. Granted having the game take the strain put on pieces and risks of structural failure into account may be a bit too realistic and may require too much work.
I found an alternative solution that may be more elegant: Welding strength.
The idea is that any piece of structure, weapon, or other part have a welding strength: This is a value given in HP (should probably be around 5 give or take depending on the part, maybe higher for weapons so their supports are robust) that is extra HP given to pieces around it for all welding point they share. For instance a cannon placed on a surface using a full 4*4 grid will give the surface 16 times it's welding score in HP and the structure will do the same (the weapon will probably have a higher welding score making the structure that support it fairly hard to remove). An exception : For balance reason, pass through parts recieve only a part of the HP (same as the damage they recieve so a 90% pass through part will only recieve 10% of welding HP). And last: If a part is destroyed, same as the cabin lose the extra hit point from structure destroyed, all parts welded to the part lose the extra HPs it gives.
The result will be that for instance the supports of weapons will be a bit stronger preventing them to be too easy to disarm. Core structure parts would be harder to destroy due to the high number of parts linked to them. And parts left hanging will be easier to destroy which makes sense and avoid aberrations. Also hiting somewhere you already did damages will be more efficient because the missing parts will mean that the parts around them that should be connected will already have lost the bit of HP thay gained due to welding.
Parts should of course have less HP to compensate if it's implemented. The idea is that a part with a reasonable number of it's welding points used should have around the same HP as right now.
I know that would require to rebalance many things, but I think it would both make builds more realistic looking and allow player to choose which parts of their build they really want to protect which can be very interesting; Placing parts with higher welding values around the structural parts or modules they want to protect for instance.