You just don't make your guns big enough... beams dont sim penetration well because of how the beam subdivides 1 shot into 5 damage bursts
That being said that is actually another advantage to beams over cannons. simply put beams and cannons will do the same amount of HP/shield/armor damage, but where a cannon will trash a proportionate amount of blocks a beam will sink all that damage directly into the ships HP preserving precious salvage!
simply put beams are more reliable for hit rate, hitscan, same DPS vs hp points, lower penetration(no over penetration), and leave you more salvageables, and less laggy.
whats not to like about beam cannonades?
from a mechanical(non-RP) perspective they are the most munchkined gun
that being said im still partial to the Swiss cheese effect large cannon/beam guns can do
and you still need like 1000/shot machine-guns to chew up the structure of a ship that you have de-armored