Just looking over the ships, few things of note:
-Hidden mounts cannot be disabled and are generally only used on fighters and in extremely rare cases on some ships, Most of your ships need to be redone with more conventional visible weapon mounts.
-OP budget for ships is all wrong. The guideline in DR's old modding guidelines post is a good starting point
http://fractalsoftworks.com/forum/index.php?topic=9052.0-several frigates are statted as destroyer size hulls. Stat lines in general are all over the place.
-Starsector is typically not to-scale. Most of your tiny hulls should be scaled up to the point where they can accept regular mounting options. (the YT1300 in your mod is the most egregious example. this is way too small.)
-Weapons should be balanced to vanilla statlines, because, well, you should consider we can just take some of these weapons and put them on vanilla hulls to make incredibly broken builds.
Fix:
Flux costs+Flux efficiency
OP costs. (I see this is next on your list of things to add, but I'll note it anyway)
No excessive weapon ranges for mount size without significant drawbacks
Missiles typically have limited ammo
Wing size of fighters shouldn't be too high if the fighter is very powerful. Amount of power-per-bay matters.
-Too many guns in general. Unless you're making a total conversion you should convert ships weapon loadouts to reflect their IP counterpart, but not copy it directly, in order to work inside starsectors ship design space. This is easier when you don't use hidden mounts, as you need to have room for your weapons and have the ship not look bad at the same time. Use vanilla weapon sizes for reference.
-Excessive amounts of built-in hullmods. It clutters the list and removes most of the thought process from ship loadouts if you're already given almost all the options you could think of having. 1-2 is normal for a faction ship, 3-4 built-in hullmods is rare.
-Fighter chassis storage hullmod is reserved for stations.
Overall: This mod needs a lot, lot, lot more work