I'm not sure there is a problem with spinal weapons - they may be working as intended.
It would mean armor 'works twice' against them, but I believe it's a matter of balance and the way armour and damage multiplication work.
Let's compare: In the old High Guard, the smallest particle spinal did 1DD damage, which on average added up to 3,000-4,000 damage (can't roll 3,5 on 1D6). Armour was practically irrelevant.
The new High Guard changes the base damage to 8D, for an average of 28 damage. Let's assume our target has armour 10. That leaves 18 damage after armour. 3% damage reduction per point of armour means 30% damage reduction, 0.3x18 = 5.4, let's round up to 6.
18 - 6 = 12 final damage, multiplied by 1,000 gives us 12,000 damage. That's three times as much as the previous version, against a well-armoured ship! If the % reduction hadn't been there, the damage had been off the charts!
But why not just lower base damage? I believe it needs to be high, like now, since armour and screens reduce the raw dice damage, and the damage multiplication doesn't happen until it's time to apply damage, meaning armour and screens are actually somewhat relevant even against spinal weapons.
TLDR: Working as intended, imho