I find it somewhat confounding that the Scarecrow has less armor than the Eagle it's based off of... As a low tech "upgrade" over the Eagle, a cruiser with 1000 armor, I kind of expect it to have at least 1k, maybe even 1200 armor. Perhaps it's a balance reason, but shaving off a couple of the small hybrid hardpoints and a few op could help keep it in line.
Also, as someone who enjoys playing low tech, low tier ships, I've spent a lot of time playing with HMI ships. I'd suggest adding ~20 op to the "Junk" combat superfreighter, and setting it's armor value to somewhere around 800. It has some potential as the flagship of a salvage fleet, where speed isn't an issue but combat capability is useful. Currently however, It's poor flux stats hold it back. I buffed the armor to 1k (I since reverted to 800) and armor/ hitpoint tanked when my flux got too high, allowing me to out-bulk most cruisers, something this ship could excel at thanks to it's module repair ability. Lacking any decent armor kind of holds it back at the one thing that could be it's redeeming quality in combat. 500 armor just isn't enough on a capital ship designed to see actual combat, even the Astral has 900. It's a little starved for OP and armor, having destroyer grade armor and cruiser amounts of OP. Perhaps it's intended as a non-combat freighter, but that would seem like kind of a waste to be honest, and we already have the Atlas for that.
Loving your mod by the way, keep up the good work.