Since the raiders are based on the dark eldar, maybe it would help to give them a more stealth/sneaky design? Make the ships slower, maybe even a bit lower tech at least when it comes to engines, but give them reduced thermal engines and cloaking devices?
That's not purely a flavor suggestion - if the ships are lower tech and spend tonnage on cloaking devices and less on engines, then they'd be less of a standup fight threat - one of the concerns I saw was that escorting your freighters doesn't help if they can easily smash aside an escort. Stealthy but weaker ships means they're still a threat to soft targets but less likely to overwhelm your actual military.
It's probably late in the cycle to make major changes, but if Steve wanted to I can't help but think they'd also be a great use for a new weapon I suggested awhile back - a shield/armor penetrating missile that destroys/disables engines in the same way microwaves target electronics. They're supposed to be pirates so this would work towards the idea of disabling and boarding ships while being less likely to vaporize a battlefleet.
The 186 torpedoes all missing also makes me think it might be worth considering a change to how ECM/ECCM works. IIRC, currently if you have a 30% chance to hit, 20% worth of ECM reduces that to a 10% chance; when the ECM % exceeds the base hit chance you get situations like the Imperium is facing. I wonder if wouldn't be better to make it multiplicative, so a 20% reduction to a 30% hit chance would be 30% * (1-.2) = 24%. To make up for the reduction it might be good to increase the effect of each ECM tier to 20% and make them cumulative, so a two tier difference would be (1-.2)^2 = .64, so a 36% reduction.