In the Description of the Empire race bonus it says it gives you 1% more main weapon dmg but the dmg on the t1 mk II Plasma Gun is increased by ~ 20% on my Dagger
Is this intended?
Depends on your synergy levels with the ship as well as any skills you have, afaik.
Also, be advised some ships have natural main weapon damage buffs. To see these hover over ship icon and hold the shift button down.