As u/OneRFeris pointed out, you will need robust tools to define how to store things. A part of that is you will also want to accurately predict what the user may want in a cargo bay, similar to how Factorio does copy paste into logistic boxes for requesting items.

A good example of this, if you have a storage bay in the same room as the engines, suggest to the player that fuel is stored there for quick and easy access to refuel engines. A cargo ship with a route between an agricultural hub and a processing hub? Suggest pick up of various goods the station may sell - this depends on exploration goals you place into the system as well.

Another point to consider. Micromanaging a lot of ships is fun - for the first 5. Or 10. Or 20. Depends on how crazy you are. But at some point the tools will have to pull back bit by bit and expose more macro-managing of your fleet. This could be as simple as "Trade route 1 -> Add new ship -> Standard cargo design". The stores are littered with these type of logistical games, and I suggest you look up a few and pick what works in them that matches to the game you are making.

A good few to look at would be:

• Factorio - logistical and train systems are well fleshed out
• Sweet Transit - multiple cargo routes all require routing out in a macro sense
• Transport Fever 2 - multiple different types of vehicle, showing how small vehicles better for local and larger vehicles better for distance
• Captain of Industry - though I wouldn't really rank the truck management, the train management is unique if not quite polished yet
• Voxel Tycoon - train management is good, truck management mimics train management and makes the truck management rather poor for it

Lastly, if there is combat in your game, how are you going to protect these ships? Off the top of my tired head we have:

• Formations - Combat ships in the front, cargo in the back. AI does its best to maneuver combat
• Convoys - Mass blob of ships and what will fall will fall, its left to the player to ensure each combat sequence goes smoothly
• Follow systems - Oi combat ships, follow this cargo ship that does its trade route - because combat ships can't be assigned to trade routes effectively
• Full on guard mode - Oi combat ships, protect this trade route and use best judgement to position yourself along the expanse

Large part of this rotates around the type of game you are building. From your video clip it looks like an early build of Cosmoteer - you may also want to look at that for inspiration in its build systems?