Idea(s)
Shriller / Driller / Drax / something
Shoots large drill that upon impact will drill through the ship, spitting out bits of shrapnel as it penetrates.
Impact Armor
Armor that when receiving an impact (aka damage) absorbs some of the kinetic energy, (maybe transferring to an impact generator or power storage), powering devices near or around it.
Hammer of Dawn (Yes, from GoW)
Now you could do this many ways im sure.
The one idea that comes to mind for me is
A - Make it so the weapon needs to have at least 2-3 beam targetors on the ship/craft (could be as simple as a dish as a turret, or roof mounted even) These would then have to either target the enemy craft before the main weapon can fire, or they could fire onto a power inlet on top of the main weapon, to charge it before it can fire the beam. Just look up hammer of dawn.