Obviously the answer is to make the entire ship out of compressible fluid.

Yes, but I wouldn't store either in bulk tanks on a spacecraft.  Carbon disulfide seems rather useless, and tanks full of ethanol near military units have a disturbing tendency to suddenly turn up empty.  The Soviets apparently had serious problems with military units becoming disabled because the alcohol hydraulic fluids had disappeared.  This was great for NATO, because it disabled both the soldiers and the tanks at the same time.

Carbon disulfide is a great non-polar solvent. Why you would need this is beyond me, but it is.


On ethanol:
Since when was any navy ever completely free of alcoholic beverages?

Carbon disulfide is over twice as compressible as water, with ethyl alcohol more compressible still.

They still aren't very compressible - carbon disulfide decreases in volume by 94 ppm per 1 ATM increase in pressure, and ethyl alcohol by 111 ppm per 1 ATM increase in pressure.

Very compressible liquids.

Air(gas) is the best medium to send force through. You will mitigate a lot of the pressure waves caused from damage if you do evacuate the air before combat. There is also the fact that air likes to rush towards an area with lower pressure, and with space being almost nothing, the air in your ship will like to go out and play when a new window is opened in the side of your ship .

It's not even remotely the best medium to send force through.  That's liquids.  But it's a much better medium than vacuum.  Blast and fire are both nearly eliminated by getting rid of it.

• Free-floating maintenance vessels are for MAJOR repairs. The kind that can still be done out of a shipyard, but not really by a small bot (or several) on rails.
• Solid State Drives FTW

For the first, I doubt there will be much work of that kind.  And working in zero-G is a lot harder than it sounds.  Particularly because thrusters tend to be things you don't want to stand in front of.
For the second, a lot of missions do use those instead.  It was an example of how this sort of thing comes up in real life.

Because electrolytic capacitors have electrolytes in them, meaning that the capacitors now have to be made strong enough to keep from bursting under the outward pressure.

1. Why are we using electrolytic caps?  We have supercapacitors.
2. So make them stronger.  It will be easier than pressurizing large sections of the ship with nitrogen.

True, and turrets don't even need to have sophisticated systems on board them that way either since the sensors and fire control are separate components. Except for CIWS, because CIWS are weird.

That's exactly how CIWS work today. 
 

I see no reason to depressurize the entire ship during combat. It should be heavily compartmentalized, yes.

• Crew are almost certain to work in shifts, meaning about half the crew will be asleep at all times. You can't depressurize a significant fraction of the living areas.
• Many electronics systems can be air-cooled. Cooling things in a vacuum can be difficult (not always)
• Selfcontained vacuum suits and tethered vacuum suits each have their own problems that would make them highly inconvenient. I don't care how high-tech you are, the breathing requirements of a human aren't going to change. Breathable air takes up space, and tethered systems severely limit mobility and get in the way of other people.

1.  You depressurize when you're headed into combat.  It would be the equivalent of a modern warship's general quarters.
2. That's a very solvable problem. 
3. True.  But air transmits damage really well (I did a fair bit of research into this, and it kept coming up even in the context of airplanes, where you can't exclude it), and I think the penalties are outweighed by the benefits.  Lack of air also makes sure that no fires get started. 

For some reason I think of ships in Aurora being a "living area" that is pressurized inside an unpressurized armor shell.

You're probably not wrong.  Pressure vessels are relatively heavy, and nuclear reactors are a lot less pleasant to be around than combustion engines. 

It would probably be a very interesting balance. How much of engineering would you keep pressurized and at a comfortable temperature to allow easy crew access, and how much would you expose to space to save fuel/air/energy?

Mass is the killer here.  I expect a lot of the work would be done with waldoes instead of men.

It should not cost much: space is an awesome heat insulator, and air should leak on a closed ship. I guess the mothballing process would include thorough sealing of all entrances and airlock.

You'd want the vacuum compartments vented.  Designing for both atmosphere and vacuum is harder than designing for one or the other. 

Again drawing from my own visualizations, those portions of engineering bays which store more important components and things that require frequent replacement would be pressurized with regular atmosphere allowing for quick easy access. Everything else would be either pressurized with non-recirculated inert gas (nitrogen or argon) for vacuum-sensitive components, or open to space. Large components would be stored in zero-g and accessed via a system of robotic arms or similar. Also, I see all exterior and within-armor-shell-but-still-in-vacuum maintenance being done by "Space Odyssey 2001" manned pods, similar unmanned systems, or robots running on tracks built into the ships.

You're unlikely to see large areas pressurized that aren't human-accessible.  Things like hard drives get boxes with atmosphere (they use aerodynamic forces to fly the heads over the disks), but the boxes are as small as possible and are treated as part of the hard drive.  And I expect that rail-mounted robots will dominate.  They can be smaller than humans (if the equipment isn't setting the size of the access ways, this is important) and are fixed to the hull instead of having the nightmare problems of flying free.

Capacitor banks and power systems would be pressurized with nitrogen or argon and recirculated to remove ozone for increased component life. For some power systems, dedicated LN2 or ammonia cooling systems might be required (lasers and associated capacitor banks, large targeting computers, sensor arrays, battery banks), for others (less powerful computers mostly) the inert gas atmosphere would also be cooled.

Why not just depressurize them?  Atmosphere transmits damage surprisingly well. 

Crew areas in exposed weaponry (turrets, missile launchers, etc.) would be normally depressurized, pressurized for crew entry, and sealed and depressurized during combat. The crew would wear full EVA suits with MMU's readily available and an escape hatch should the turret be irreparably damaged, but until evacuation was necessary they would be connected to life support ports integrated into the turret or similar.

I'd just keep them depressurized and use air locks.  But I wouldn't put crew near the hull in the first place.  It's expected (and appears to be how Aurora works), but even today, naval crews are usually quite a ways away from their weapons, a trend that will only continue in the future.  The crew will be deep in the hull, as safe as possible.

On very large ships, especially those with long deployment times, the agroponics modules would be pressurized with an atmosphere specialized to the crops being grown, and serviced by an automated system. Crew would wear oxygen masks for entry and manual servicing and harvesting.

Makes sense.  Those are probably going to be the only things kept pressurized in combat.  And their design will be a sure sign of real vs fake navies.  The real ones will have theirs heavily compartmented.

And yes, I overthink things. I should write a short story about a single battle in my envisioned spacecraft.

You're not the only one.  I wrote a 150-page paper on space warfare.

I quite like picturing ship beind depressurized for combats. Fighters wouldn't even need a cockpit, you could have the pilot exposed to the outside.

How long are you planning on keeping the pilot there?