A percentage reduction could work quite well, even an opposed check of tech level of armour, tech level of installation or construction vs tech level of weapon. Higher tech weapons may have a beter chance of getting through armour. intense focus, high yield or other new advantages may be possible for higher tech upgrades to weapons.
New Hull options in addition to reflec or radiation shielding could be created. Ablative, particle resistant, meson resistant, superior radiation resistant, ion resistant, crystal infused, Jump focused etc etc. Some may stack, others may not (like reflec and stealth for example).
2% per point would max out at 30% damage reduction. Is that enough? Could it be pushed higher? I am thinking of slabs of superdense plating, or the batestar galactica scenes of nukes going off and the ships just continuing to fight.
Spinal weapons of massive power needs and armageddon level damage were developed to crack the armour of ships that shrugged off everything else shot at them. These weapons stood a chance of hurting the massive ships.
On a different note the negative DM's of the spinal weapons. For the cost of the targeting computer and software it would be worth buying a sensor array and targeting computer running fire control 5 just for the spinal weapon to give a good chance to hitting a smaller ship if the 5k spinal ships became an issue. A dedicated computer system would be worth the extra expense if it allowed for one shot kills on those pesky smaller ships. This would open up an entirely new area of ship design, cost and e-warfare avenues. Just a thought.