I think they're awesome - I enjoy using them, but. They present issues in that the use of them is purely a player-facing thing.
The AI fleets don't need to make profits, they don't have to worry about purchasing fuels and supplies, just that they've got enough stored that if they make it into the Zone of Realization around the player where they move from abstracted to real, they don't run out of supplies before messing with the player.
Civilian ships don't have enough ordnance points to have a combat setup (weapons, vents) and campaign hullmods.
Yet this doesn't matter for the AI fleets as almost none of them affect them (yes, it would be vastly annoying to have a hostile fleet with all augmented drives), which means that any of the combat freighters they field have what is an effective advantage of 40-80% more OP dedicated to combat stats than your vessels, if you even bothered to outfit them.
I believe some changes could be made to them so that while they still might not do anything useful for the AI, it would feel much more fair to the player to actually take advantage of them.
Basically - every ship could get a paperdoll like equipment slot system, with engines, armor, interior (cargo/fuel/crew), and so on. More exotic slots would be available on more specialized ships, surveyors, salvagers, tugs (which I'd like to see more of, as they're a neat concept but enormously overpriced for the player to use simply do to their overhead eating your cargo space), but everything would have a basic layout.
Larger vessels get more slots, whether it be additional space to mess about with efficiency or multiple exotic slots to play about with.
These would default to sensibly desirable hullmods that, if the AI fleets were in the hands of another human, you'd expect to see - expanded holds, increased engine speed, efficiency, and so forth. Thus, on ships that you salvage, you'll actually find loadouts similar to what a player would field.
Changing them would require being docked and knowing the hullmod blueprints like you currently do, but instead of costing OP, installing them is a credit cost.
And finally, they wouldn't immediately require a large additional amount of work from modders as each hull class (and type of ship tag with freighter/tanker/combat) would come with the default slot layout and loadout.
There's of course tons of other ways to quick and dirty make them not so imbalanced towards benefiting the AI, making anything tagged with campaign hullmod cost 0 OP, but I feel that there's lots of room here to add more fun customization options with an implementation like this.
Also I just really want to be able to spend credits to buy OP so I can actually fit my Apogee with guns. I love flying it, but it can barely fit front weapons and it's mediums with two combat hullmods, let alone actually have anything in its missile and PD slots.