If I remember correctly there are only a few ships that gain a sudden boost in missile compatible mounts (Without ship specific changes to balance things out.). Ill look into tweaking them directly before looking at the pirate modifications hullmod as to not blindside other ships by accident.
These ships got lots more missile but without more DPs:
Brawler (TT), 2 M-Universe + 2 S-Universe
Mule (P), 3 M-Universe
Hammerhead (P), 2 M-Missile + 2 S-Missile
Fulgent (P), 2 S-Missile + 2 S-Synergy + 2 M-Synergy + 2 M-Composite + 1 M-Universe; 5 middle missile + 4 small missile? No ideal how to balance this...
And I think mudskipper can arm with big missile is way too much, big energy is fit its original design -- barely rubbish, bug big missile with only 2 DP...
Besides,
Derelict Master can be scavenge and only 11+11 DP is really INSANE, this ship is strong enough to kill several cruiser without much trouble. It should become some secreat tiny boss, just like a small version of Guardian -- which cannot be scavenged. Some people even think it worth 40DP...