Dragleones pointed out a few things I was thinking about as I read through the original posts.
1. How will this affect astronaut inventory? It must lower it, otherwise no one will use the cargo/storage systems. If it lowers astronaut inventory capacity, how then will I transfer huge amounts of cargo from a freighter to my station's cargo hold?
2. If I am working on a new ship (just a ship core), the only inventory I have access to is the astronaut inventory. Must I use Astronaut inventory to build a ship cargo space so I can then fill the cargo space to have enough blocks to build the rest of the ship? Or must I enter/exit build mode a dozen times to restock my supplies?
3. If I am mining/harvesting and I have a hard-coded inventory capacity I am forced to go drop off goods. This means that harvesting trips will be a lot of back-and-forth flying through empty space, and a lot of walking to and from my ship to transfer cargo to the station.
4. Faction permissions will need to be implemented to control who can access which cargo holds. If my player cannot carry the millions of blocks I've bought/built/found I have to store them, and if I store them I need to protect them from unauthorized use - especially within my own faction.
Don't get me wrong, I really like this idea. If I go into battle with a freighter and destroy it, I should be able to salvage the cargo instead of the pilot dying/teleporting away with it all. And if I missile the cargo hold then it should destroy cargo blocks (as sad as that would be). And blowing up Isanths should not produce a cloud of items that has hundreds or thousands of mass that I collect by flying through.
So however we go about limiting cargo capacity/inventory we have to make a way of transferring cargo. This could be as simple as a Cargo-Transfer Beam. Each Cargo Module has a beam like a ship core that can target another Cargo Module (or module enhancer connected to a cargo module). Upon connection the two cargo modules are opened so a player can transfer items between the inventories.
This will allow ship construction to access station/freighter inventory with the push of a button so long as the design keeps the modules exposed for use.
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Schema has said he will be implementing a ship yard to construct ships, and that there will be an expansion of Astronaut play. The way these features are implemented may have a huge impact on the way inventory works. I've also read that moving parts will be implemented at some point - cargo bays that slide out of one ship an into another sounds nifty.