While the railgun loader holds up to 6 shells ready for use, there is no means to store additional or surplus shells you would craft or buy from the store, instead laying about the cargo section of the ship and vulnerable to being knocked about by a collision or enemy impact, which is dangerous and not to mention does cause performance issues if there is a lot of them. While some of them can be reused and recovered from combat, most occasions they are lost in the abyss of the caverns.

So in addition to the loader, there should be a railgun shell rack that acts the same way as a loader but is vertically designed to allow storage up to maybe 6-7. Which would be help store them away and ready for reloading the railgun and also eliminate additional physics objects from your sub to prevent FPS issues. This could also allow additional benefit to store certain nuclear or volatile loaded shells that you want to keep for certain situations and away from any unexpected bumps. The same could be applied for Depth Charges also as the loading bay only holds one (if not a depth charge storage bay, maybe a larger loading unit in addition to the singular version ?), so the same problem applies as the shells. I suppose there could be two versions. A singular rack design that holds one shell for smaller spaced areas and the larger version which height covers a door space for most common sub corridors.

The same could be applied for weapons like the harpoon gun, a object to hold the gun itself and a separate one to hold any extra spears that are lost during combat outside the sub.

Later on in development there could be a more advanced version of the loader ? That stores a larger amount but requires power to reload a shell after each shot, and if power/load ratio isn't maintained, it could short out/start a fire, which could be dangerous if it's loaded with explosive or nuclear payloads.

I second this. Would be very helpful and look super cool.