Yeah, been going through today and doing some balance shifting to bring SHI's stuff more in line with the new vanilla balance. Fighters were one of the things I touched on.
Also regarding this:
I did set the relationship between the church of galactic redemption and SHI to be inhospitable, actually, but for some reason it's not taking.
I believe I've determined the issue - having strained but still peaceable relations is not enough to make one an enemy, and as such, while the Church of Ludd and SHI may distrust the hell out of each other, my best guess is that as long as they aren't shooting at each other the player doesn't receive that information. Setting them to hostile for now.
New dev build time:
Fixed a bug that was doubling up the economy (my fault, really, was just fumbling about trying to determine how to get the economy to function), and added a faction description/changed some of the background info slightly. Fiddled with missile balance and made all the ships cost an appropriate amount. Also added a portrait that I forgot to put in last time.