I disagree, while those ships are indeed under-armed. They still fill the role of support ship, like the Condor in Starsector. The Iconus could be a very interesting addition in the game by adding a drone shield system which would work like the shield projection. Just like that:
The Revelation is still decently armed, i counted 6 guns, 7 if you had the bombardment cannon. The clairvoyance ability could be interpreted as a ship system that increase the radar range during battle, like the sensors drone of the Apogee.
The Solanus isn't that tricky, it just need a new personal weapon. A modded short range MIRV with the sprite of a Flare will do the trick.
The Domina Subjugator would probably be a simple EMP support destroyer.
For the TEC, the Cielo got "Designate target" which increase damage. Shouldn't be too difficult to make it a ship system, the Hauberk from the Kadur Theocracy mod got a similar system that buff the range of your fleet.
I don't know if is possible to replicate something like the Hoshiko's reparation system, might need to ask the scripts wizards of the forum. Alternatively the Demolition bot should be pretty easy to do, basically kamikaze drones with EMP damage.
Also, how about converting the constructing frigates from the game as tug boats?
But yeah, please don't overlook the "crappy" ships. Even if they will lack firepower in the mod, they'll make up with fancy support systems. I think that's really where your mod could shine.