There are a couple of ships that are scavenged sometimes that are basically useless in combat. One is a yellow ship whose firing weapon has no range and another is a canon looking ship.
If we could get the reverse-engineer the basic designs of these ships we salvage and change the weapons for some which we have obtained during the game. Could be the super-nuke, the plasma, the death ray etc. Then the player could retrofit these ships so that they can become useful.
One ship for example fires a spray from the back but it has no range I'd replace that weapon with a plasma and put a death ray on the nose.
Some ships may have good weapons but a poor crew complement, I'd swap their weapons on a ship that has a big crew quarters and bad weapons. The Starbase could be a chop shop where various combinations could be made from ships that are salvaged.
Also, I don't get why we don't get hyperdrives from those salvaged ships.
I do agree that there are some weapons which are relatively worthless and do not seem to compliment the ship's primary weapon well. The Tywom's primary gun is fine, I personally believe, as its mainstay is launching drones, and any further improvements to its main weapon would make it a bit OP for its fleet cost (after all, I only really use the primary weapon as a dire last resort, I don't think it is really intended to be the mainstay for the ship). One ship that I do think has a poor complimentary weapon system is the Caster, which has the laser bolt and the scout shot, the latter of which is utterly redundant as it has no real advantage over the laser bolt. I would propose either replacing the scout shot with something else (maybe a rearward shot to at least compensate a bit for the mediocre agility of the Caster? Though I am certainly not sold on my own ideas at present, so feel free to pitch in). The scout shot itself feels out of place on most ships it is found on, so I would almost suggest a revamp of it to give it substantially more range and speed, but to cut down its damage (after all, it is supposed to be a scout shot, which implies to me a relatively weak, but fast-firing and long-ranged weapon).
The cannon ship which you described is also a pretty weak candidate, I agree, but I don't know what could be done to improve it properly, maybe an increase in battery reserve and recharge rate?
Lastly, the salvage idea I think is quite clear why it is not present in the game, mainly due to balance considerations. Though I do think that if later on if there was some way to reverse-engineer these weapons it would be quite neat indeed, though early game I think it would greatly hinder balance instead of aiding it.
The last thing I wish to address is the super melee ship customization which, while exceedingly enjoyable and a lot of fun, seems to be lacking the full breadth of weapons available to all ships in SCO, which is a shame because there are some incredibly enjoyable weapons in this game that we cannot play around with in super melee. I'd love to see these weapons added (along with parts of the ships that have them if they are indeed missing) even if it takes some time to balance out the fleet costs of each weapon, I think it would just greatly add to the longevity of super melee as a whole!