The only hullmods I had difficulty finding was Integrated Targeting Unit and Converted Hanger - though I will say I don't find Converted Hanger to be *too* useful. ITU though, is very - eventually got both, actually, from a particularly juicy Research Station salvage. Every other hullmod was purchasable from some station, either legally or illegally, without really having to delve into Military. You tend to go to a lot of different faction's stations when you explore every corner of the galaxy - Persean League, Tri-Tachyon and all the rest. Furthermore, exploring in and of itself tends to give a lot of hullmods, especially finding Abandoned Mining Bases, Research Stations, and Orbital Habitats. Oh, and I just got an ITU Modspec drop from nuking a Persean League merchant convoy. I suppose you can go and delve into the code to see what faction generally equips the hullmods you want, then go hunting their fleets for it.
That's my experience at least, never really had problems from my very first save.
