@Gothars: By 'magazine', I don't think that folks are meaning detachable box magazines, but 'magazine' is the generic term for the place where ammo is stored; whether that be in the ship's main magazine or ready to use in the mounting itself. It's 'clip' that has the specific meaning: a strip with some rounds lined up in it that is then inserted into the magazine - from there you push the rounds into the magazine and remove the clip (usually; sometimes the clip gets ejected in some other way).
You see this mostly with WWI/WWII rifles, before detachable box magazines were commonly used.
@JT and generally: How ammo is dealt with in ships is mostly down to how powerful that ammo is, what would happen if that part of the ship were hit with that ammo in it, and how much mass and expense it takes to armour the path that the ammo travels. Smaller rounds can be stored in the 'turret' (cupola) itself; main gun rounds tend to be kept (with powder charges and projectiles kept on different decks, both comprising the magazine) deep in the armoured citadel and hoisted up to the turret as needed, with heavy doors to prevent a hit that penetrates the cupola sending a flash all the way back into the magazine.
[There's some evidence that part of the problem with some British capital ships exploding way too easily in WWI was that there was an obsession with having a higher rate of fire; so orders were sent out to cut safety corners to this end. Main gun ammo may have been stored in cupolas and some elevator blast doors may have been disabled in order to get that RoF up... but then what should have been fairly 'minor' cupola hits detonated the ready ammo lying around and sent an unopposed flash right down to the magazine. There may have also been a problem, at around that time anyway, with the cordite being stored for too long, but we'll probably never really know for sure... though it's sure fun reading naval historians debating this.
]
I can imagine that most of the Starsector gun mountings will follow the design of some of the slicker mounts used today (eg OTO-Melara 127 mm/64 LW), as mentioned by JT, where there are ready to use magazines in the cupola, that thus offer a temporary high RoF (or/and instant selection of different types of rounds); but the below-deck main magazine is still the usual one (the most heavily armoured part of the ship) as described above. Once you've fired off the cupola magazines, then feed/RoF is slow from the main magazine, and if there's a break in the fighting, the cupola magazines can be refilled... though this takes time.
The very powerful cap ship main guns (if chem powered) would follow the more classical battleship feed system, for the same reason. But this then makes the magazine a point of catastrophic failure (that costs loads of mass to protect properly), so if these ships can manufacture ammo in a more mass-efficient way, rather than store loads of it in magazines, then that'll defo be the way forward.
It may well be more efficient to manufacture clips of ammo, which then get fed into the magazine; the number of rounds in each clip being governed by that not being catastrophic for the ship if any part of the system that feeds that clip to the magazine gets hit, which will be linear with the gun's power. In other words, what HartLord wrote:-
I think the way this works, is that instead of a central magazine, they have an autofac. The autofac produces clips of ammunition, which are then loaded into the individual guns' magazines.
Just a few thoughts in terms of how the mechanic could work, continuing the high verisimilitude/immersion of the game... I'm sure Alex has bigger fish to fry, but it'd save him a lot of future angst from purists
if there's even just a tiny bit of flavour text that shows that the 'clips' being mentioned actually
are literal clips.
Cheers.