Gents,
Interesting topic and interesting posts as always.
I look at the problem from a different angle because, as you all know, I'm weird.
First, tell me, on an average voyage how much time does a merchantman spend in normal space? Not the PCs mind you, they're always the exception. How much time does a merchant spend in normal space?
At one gee it's ~6 hours to the 100D limit of an Earth-sized world, although stellar jump limits and jump masking can certainly add to that. At one gee it's ~18 hours to the 100D limit of a gas giant too. You add those travel times to the time spent in jump space and your average merchie spends well less than 10% of their trip where someone can shoot at them.
Next, how long of a fight is the average merchie going to put up? Are they going to be in long fights with lots of missile salvos and lots of reloading? An HG2 battle has 20 minutes rounds, so those three missiles staged for each launcher in each turret are going to last an hour. A LBB:2 battle has 16.7 minute rounds, so those three missiles are going to last 50 minutes. A Mayday battle has 100 minute rounds, so those three missiles are going to last 5 hours(!!!).
Is the avarge merchie going to fight a battle long enough to even require missile reloads? And how many merchies are going to be throwing lots of ordnance downrange when each round is nearly the cost of a middle passage?
Let's face it, Captain J. Wellington Milquetoast of the subsidized merchant Carol Channing flying along his route in the Arglebargle Cluster isn't going to be involved in multi-hour, ship-to-ship, donnybrooks. He's not going to stand toe to toe with an opponent throwing missile-heavy haymakers in an attempt to knock the other guy out.
When he does get into a fight, he's going to use lasers because their "ammo" comes from his power plant, he's going to use sand because it's cheap and protects his employer's ship, and he's going to fire the occasional missile to keep the other guy honest. When he does get into a fight, he's not going to fight for long either. He knows it's going to take hours for the other guy to match courses to board, he knows he just needs to delay his opponent for an hour or so, and he knows that most systems will have SDBs and patrollers thrusting to his aid. He's not going to need to worry about reloading his missile launchers during battle because he's not going to use that many missiles and he's not going to fight for that long.
The players, on the other hand, are another kettle of fish.
Players are going to use missiles like kleenex, fight lengthy battles, and bend every effort to curbstomp their opponents. The OP's question is not how missile storage and reloading are handled aboard civilian ship. The OP's question is how the players want to handle missile storage and reloading aboard their ship.
Normal civilian ships make little provision for easily accessible extra missile storage and rapid reloading, so it's up to the players to refit their civilian ship to provide the same. Make them determine where and of what size missile magazines are. Make them also determine how reloads are moved safely and at what speed between the magazines and turrets.
This is chance to encourage roleplaying by the players. What's more, the solutions they create will suit them far better than any GM imposed system or table look ups.
Regards,
Bill