Summing this up leaves me with a question.
You plan on implementing a storage system attached to storage blocks. For each stack you will probably need one free space. So a 2x2x2 cube could store 8 stacks of material. That could be 8 stacks of 1 material or 8 stacks each different. Potentially that stack could be limited by mass or count from what has been said so far. The size of a storage could range in 3d space from 1x1x1 to XxXxX X being whatever size or limit you may put there.
That said each new cargo container that fills up that space will be a block and have mass. Thus now every single ship / space station ever made that has storage just became obsolete. Because now you have to account for the added block count and mass of the storage as well.
Don't get me wrong some aspects of this I like a great deal.
However this is going to mess with everything from power to shielding to you name it that relies or is tied to block count and mass.
Ships are going to have to be massive in a game that already is hard pressed for space because we don't have thin walls like in RL but here you are trying to add a feature into the game that in a way mimics RL to a moderate extent.
So my question would be what changes are we going to see to power, thrusters, shielding, Effects, jammers, cloaking... and all the other items that block count and mass is tied into to compensate for this change?