Yeah, I've never heard of a light mortar on a bomber - Do you mean Nova Antimatter cannon? (OR as I like to call it, the NAM!)
I personally would love to see more fighters loaded out from a Role Play perspective. Granted I will admit that on my BHG Character I am currently using two Salamanca MkII's in my class 9 slots on my Manta VHF - but in that case they are guns I looted from killing my enemies. The rest of my loadout though, is not populated by any BHG weaponry, which is something I intend to change.
As far as loadouts go, there are some incredible loadouts for all the factions. I've been taking a look at all of the class 7-9 weapons and surprisingly there is some NASTY damage to be had by those, from all factions. The only thing we are lacking weapon wise is shield busters that are civilian and have a range of projectile speeds. We have 750ms, we need 700 and 600ms as well.
As far as capital ships go, I agree, mount the weaponry available to your faction. Igiss balanced the capital ship weapons very well and there are only minor differences between the stats of the weapons. It's usually a difference of 5-10 damage per shot.. Big whoop right? Don't be a super PVP whore and get a gun just because of a few points of extra damage, get the one that's for your faction..
For example, my BHG characters gunboat is a Liberty Gunboat. I have it loaded out with all liberty turrets. Why? Because they are designed for the liberty GB. The aesthetics, the namesake, and the power drain. If you stick with a weapon set that is made for your factions fighters, odds are you will have little to no power issues. Just something I've noticed.