First thing's first - Thank you to Pzikhedlic for his Glorious Ghost Junk mod.  While my file is completely original, I basically learned how to mod this game by reading his.  You are a good person if you go give him an endorsement.  Now, moving right along...

Second, this is probably my most chatty description yet.  Sorry bro.

This mod makes some rather drastic - and yes, very very game-breaking - changes to ship combat.  They are as follows:

• Haeferic's Nose has received a massive buff.  It now deals 90-110 base damage per shot, which is enough to sink any ship in the game in a single blow.
• Its range has been altered to 0-600, meaning that it has standard accuracy at any range.
• Its crew damage has also been drastically increased to 20-30, which means 2 good hits are enough to fully depopulate a ship, making boarding a breeze.
• It now uses no ammo to fire so you never have to buy ammunition again.
• The Submarine Cannons are now identical to Haeferic's Nose.
  

The reason for these changes is that I got rather tired of ship-to-ship combat as a whole and yet I still wanted to do bounties, especially after you finish one of the faction quest lines and attain the supposedly "end game" ships, only to find out that the Sub's only real strength is guaranteed escape, and the ghost ship is just a reskinned Galleon that can't have sail upgrades.  Why the hell doesn't the sub have powerful guns, given it's a Rautai ship and guns are literally their specialty???  Anyhow, this mod makes it easy to jump directly to a heavily weakened boarding stage, or to skip it entirely from 400m away.

Also note that, while I prefer to just console myself one of these two ships once I reach Nekataka, you can also just buy yourself a Voyager.  Due to the forward placement of the cannon, you can stick a single Haeferic's Nose on the front (even just the one you get if you bound the souls in The White March) and then you can literally win every naval battle in a single turn by shooting on the very first turn of combat.  It's especially fun if you roleplay a Huana.

Anyhow...besides all that, I'm also including an optional file, inspired by the Glorious Ghost Junk and Glorious Submarine mods mentioned above.  The optional file does a few more changes directly to ships:

• The Ghost Ship is re-classed as a Junk (10 cannons) and has increased base hull, sails, and speed.
• It has most slots unlocked, but left the Lantern and Extra slots locked.  The reason is that equipping any non-default Lanterns or the Captain's Cabin upgrade causes serious graphical oddities, i.e. lanterns hovering in space and bright orange-lighted window panes floating behind the ship when it's docked in port.
• The Ghost Ship now comes pre-loaded with 10 Haeferic's Nose already installed.
• The Sub has similar changes.  it has the Hull, Wheel, and Anchor slots unlocked.  Sails remain locked, unlike the Ghost Ship.
• The Sub has nearly twice the Hull of the Ghost Ship to compensate for having no sails at all.  In total both are around 900-1000 total health.
• The Sub is preloaded with the normal 4 Submarine Cannons but because of the main mod those are essentially Haeferic's Nose with a different look.
  

As for compatability, you can use the main file alone with Glorious Ghost Junk and Glorious Submarine if you don't mind the graphical issues those cause.  However, the optional file (Nosejob) will conflict with Glorious Ghost Junk and Glorious Submarine, so use my optional file or his file, not both.

Also, just to make this a little easier, here are the console commands to give yourself the Ghost Ship or Submarine

iroll20s
giveplayership shp_submarine_base
giveplayership shp_galleon_ghost_ship

NOTE 1: Using iroll20s enables cheats but also disables achievements.  I personally don't care about achievements, but if you do, don't use these commands, obviously.
NOTE 2: You can run both commands and own both ships, but you can't sail both ships at once.  Thus, it's usually better to just pick one or the other since you can't actively use both anyway, or console in one ship then earn the other.  Unless you're going the Huana or Vailian* route, in which case you'd have to console both to have them.

*Also if you're going Vailian, you're a monster.  You're killing souls for the production of pain killers and profit.  That makes you a real monster.  Hell, even the Principii don't destroy souls to make their fortune.  Just sayin'