increase the "hull_damage = " and keep the radius small to 500 or less.
That should solve the problem.
Depending on how you balance the damage vs hit points (as also with cost of the weapon) it could be anything from several missles to a single sunslayer.

Do your Capital Ships have shields? If so, take them off and see if that helps you - it did for me.

The true work-around is to modify or remove references in shiparch.ini to the specific "parts" of the ship, but I'm not really sure how to explain that one; I'm sure someone else here can do a much better job of that.

No, no shields. Remove 'parts' from the shiparch entry? I don't know about that... I boosted the hit points of those parts to match the hull so that the ship wouldn't die early because a component was shot off. I'd like to hear more opinions on that one.

regarding the parts that blow off and affect the overall health of a ship, that can be changed to: root_health_proxy = false. That should limit how much a ship suffers when parts are blown off.

bump

I am experiencing the same (or very close to) problem in my MOD it appears Robo is.

I can fire off over 100 Sunslayers at a PC flyable and controlled battleship and it does mild energy damage, turret damage and no hull damage. I have altered explosion setting and got no change. Missiles/Torps damage Fighters just fine and gun fire can kill a capital ship so I know its not really a damage type issue.

I modified a Sunslayer to "fast track" (max angular velocity of 5.58) targets and do enormous hull damage of 250,000. (coupled with the fx of the Lib Dreadnought main explosion and the sound of the CSX_large) That equivocates to 125,000 energy damage. The blast radius use to be 1000 but that was a little excessive so I dropped it to 750. I didn't increase the speed of the torpedo, but rather kept that part "slow" . It proved very interesting. It will take out an entire wing of ships in formation especially at long range.

As for player controlled capital ships, depending on their hull stength (hit points)
a sunslayer could take it out unless the hit points are way above what this sunslayer can do. For some of my ships, it would take up to 12 sunslayers to take out one of those capital ships.

I also modified the Nomad rtc torpedo and gave it the ability to track (max angular velocity of 5.58) but limited its damage output to 10,000 (energy damage of 5,000) . They have a seeker fov of 180 degrees which means all you do is aquire a target and fire. They're like a very nasty "Sidewinder" missle.