When a ship core is destroyed, it can't get more damage but the projectiles fired on it will still act like they hit it. This means that systems, right behind the ship core cannot be hit (by AI) because the ship core is protecting them, it can't overheat that way either.
The projectiles should pass through it.
How to reproduce:
# make a ship core, put 1 power regen block behind it and behind that 1 thruster module
# spawn a isanth CC (cannon + cannon) weapon and let it fire on your front.
# It will not be able to kill you after your ship core is destroyed, it will keep shooting it and the blocks behind the ship core will not be destroyed because the ship core blocks all projectiles.