Love the idea.
A few bonus suggestions?
1. Cargo transfer should just go over the basic docking module instead of any fancy way. Its probably easier to implement that way and the infrastructure required is most likely already in place. Maybe with some blocks that increase loading/offloading speed for dedicated cargo stations?
2. Give the Bobby AI module the ability to set up a cargo route, the option to wait with the transport until its cargo hold is filled to a certain degree and the option to only load specific cargo. And theability for me to automatically jettison certain things (red dirt, anyone? Havent found a recipe that uses it yet)
Example scenario: I am mining asteroids. My ship has a cargo hold, which fills up quickly (nom nom asteroids). Now i could fly back to the factions main factory, but that is inefficent. So I attach two freighters to my ship and tell them to fill their cargo hold with materials, the smaller one taking minerals, the bigger one the generic blocks. And instead of flying back to the factions main factory, which (because of asteroids being further away) is quite a ways off, i have them set to go to a refining facility my faction set up close by to keep ways short and the harvesters going.
So what we have in the paragraph above is: A reason to set up frontier outposts with manufacturing capacities, a reason to switch turrets for freighters on salvage ships, a way to not have this system interrupt cracking asteroids as long as you do not get too far away from your factions territory and the opportunity to bring a bit more life to the game by having AI controlled freighters fly all over the place.
3. If a cargo block is hit by a weapon and destroyed, its gone, with all its content. That way, someone out to get the cargo needs to put a bit more effort into it (destroy thrusters and turrets, hit the core without hitting the cargo bay with anything big) and not to bring the big death star that cleaves the freighter in half without leaving cargo, while someone out to just cripple your faction blasts away without remorse, which is ok as far as I am concerned.
4. The limitation should just be an item count. 1000 a block was a number floating around somewhere, I would go lower to 500, but thats personal preference. Why just item count? Because then we have a clear efficency list on what to transport with freighters and what is just too inefficent to haul around and store for a long time/in big quantities and again, easier to implement than some evil calculation of doom.
The efficency list, you ask? Here, let me help you.
The least efficent thing to haul around and store with this would be capsules. You get 10 per mineral block, meaning that for one cargo block full of minerals you get ten cargo blocks of capsules. Pretty inefficent, huh? Better make them into something useful quick.
The next two are minerals and intermediate products (metal mesh, for example). You need a lot of minerals for one finished product and unfinished products require that the material to make them into the thing you want (often capsules) are already in place or are being hauled to the factory. Not as inefficent, and in the case of the minerals actually needed, but still not good.
And with what do we fill our cargo bays? With finished products of course. One missile barrel is what? One hundert capsules? Thats the stuff we are transporting and storing efficently. And that makes those freighters and storage/factory stations actually interesting for pirates and rival factions: They are filled with shiny finished stuff and if they take it, they dont have to worry about all the logistics around it. Especially with the addition of a drydock sort of mechanic, this will be a major point for factions: Take freighters, kill freighters, stop freighters. Everything that can stop that titan in the drydock from being finished.
And the last thing is totally optional:
A beacon block and a beacon reciever block. What do those do? Simple, the reciever goes to your station, the beacon itself to your ship. Then you align the beacon with the reciever.
The reciever can be interacted with and shows 3 categories.
First is the list of aligned ships. All you get there is that the beacon tells the reciever "I exist and I am on this ship".
The second one is a list of destroyed/deactivated beacons, with the ship name it was on and the time stamp when it stopped existing.
And the third one is for still active aligned beacons on ships that switched factions (IE captured freighters). Here it tells the name of the ship and, more importantly, which faction the ship now belongs to.
The above could help keep an eye on your factions ships, replace losses according to demand and catch some pirate/rival factions if they do not find the beacon on your ship. Aligned beacons are undetectable without visual identification, as in: You will have to dig through the ship or study its blueprint before being able to just take it home and integrate it into your fleet. Or you just blow a lot of holes into the ship and hope to hit the right place.