With a surface vessel or sub, I would imagine they would likely be solid fueled and sealed in containers, The need for this type of magazine system is for liquid fueled weapons and their various needs and much higher maintenance. Ship mounted fateh/zulfiqars would probably be like the any air defense missile system or cruise missile, all sealed in vls containers in the ships hull. The question for me would be if the tactical ballistics can be programed from the bridge, or already have coordinates pre programmed, before install; depends on how much local or centralised control the command structure would deem proper for the missiles.
Also, it would certainly be IRGC ship at first, with some cross coordination be the naval and aerospace forces. The more I think about it, I think they might rather concentrate on cruise missile for ships and subs, but never rule out options for carrying heavier weapons.
Also. a larger vessel could also serve as a space launch platform too.
Another point to add is that the aerospace forces might not want to divide control of the missiles with the naval branch or any other branch for that matter, while sam systems and radars and drones are shared by them, the missiles are a different matter and I can understand on psychological front. Also, said missiles become a bit vulnerable while out at sea so older models would probably be utilised first by the naval branch if should ever happen.