I'd think that any "warship" would prioritize functionality first. That is the Role it Plays. (see what I did there?)
To elaborate: Firstly, One must prioritize between speed, firepower, and defense. The order of these three variables determines 90% of the rest of the ship.
If firepower is priority, one muse sacrifice speed or durability, or compromise on both. The term "glass cannon" aptly describes a ship heavily leaned towards firepower. It may be a tough and slow "Mike Tyson" glass cannon if defense is second priority, or it may be a fragile but agile one with thrust as second priority.
If speed is a priority, firepower or durability must be sacrificed, or compromise on both. If firepower is your second priority, you're creating a Muhammad Ali of ships. If durability is your second priority you'll be creating a Rhino of sorts: speed(the charge) with damage in a very specialized area(the horn) and thick skin.
If defense is your priority, either firepower or speed must be sacrificed, or compromise on both. If firepower is your second priority you're effectively creating a "guard" or "peacekeeper" Slow but powerful hitters have their place, and usually as an emplacement. They're not going to catch anything running away, but they will damn-well stop anything from getting to what they are guarding and do it for a LONG time. If howerever Their second priority is speed over firepower, their job directly becomes a "Tank" or "Sponge" to use the MMO terms. They would lead the charge and draw the firepower (aggro) and then kite the trash-mobs back to a fleet. Hoping to keep the aggro on themselves so the glass cannons can fire with impunity by drawing targets though a killbox. Artificial Stupidity makes this a rather lucrative role.
This is a very viable thought process for secondary roles. In an action situation, nobody is going to be caught sleeping. I might personally have slept through a train wreck, but no way would I sleep through shots fired in my vicinity. "battle stations" on star trek comes with a "wake up you scrubby enlisted" siren for a reason. Nobody is off duty when a breach might need sealing, a blown out power conduit bypassing, boarders held or rebuffed, etc.
I personally consider all the "wetware dependencies" to be "soft armor" for the Hardware. Mess halls, sleeping quarters, meeting rooms, clerical, all of it is just "spaced armor" like you would find on a modern tank. In the end, if it doesn't make you shooty, it's something you would prefer get shot first. Even a triage area is less important than what keeps you in the fight, as no body is going to get their bullet holes patched-up to win the war if you lose this battle hard enough.
It's kind of like CPR and emergency room triage: they stress the ABCs of Airway, Breathing, and Circulation. Can you breath, Are you breathing, will you bleed out. In that order. For ships it's "can you do damage, can you avoid damage, will you overheat if you take damage".
As others have said, Aux Power serves the magazine role perfectly in every way. It IS ammo in the form of energy, and it goes boom if someone shoots it. The wisdom of placing them near the weapons is lacking in SM engineering, unless you go for "all or nothing" armoring philosophy, in which case it is VERY important to do just that.
Effectively a warship should always be, and look like it was designed and optimized, for one role. Anything that "keeps it ready" between filling that role is bolted on or wedged-in as an afterthought. Crew bunks slotted in between magazines "because there's space", mess stations just outside of a pressure door, and lavatories nestled between ballast and coolant reservoirs, are things you'll readily see in RL warships.
Now in a flighty fancy space-opera like anything Gene Roddenberry a "warship" will often be anything BUT a warship. Andromeda (a titular Warship) more often resembles a pleasure yacht pressed into service as an afterthought. Even the "warships" of StarTrek more closely resemble flying office buildings or industrial R&D wings. A warship has hallways you must plaster your back against a wall to get past another person, not a walkway where four people can walk abreast with room to do the chicken-dance.
As
Edymnion pointed out, the Defiant-class is about as close as ST gets to a true warship (depending on which of the several "official deck plan" you go by) but even it's philosophy seems to be more of a
picket ship than a true warship.
StarWars is equally guilty of treating commercial-zones-with-wings or cruise liners as "warships" and "carriers". Just look at the hallways on the deathstar or an Imperial Battle-cruiser. Again, room to tango while walking both ways.
If you want to see a Warship in cinema "The Hunt for Red October" would be a good reference, or MAYBE "2001"(despite it's lack of weaponry).
In the end, "warship" is synonymous with "cramped and stuffy" even for an agoraphobic. It would be hard to tell the difference between an "RP warship" and a bare-bones PvP ship for this reason.