If you don't directly tear minecraft's grid storage system and sprites, I'm review bombing this game.
(JUST KIDDING JUST KIDDING!)
I'd think that collected resources would still need to be transported by crew around the ship. Maybe you could drag resources to different storages, leaving a ghost of the resource in the new storage, and then await crew to complete the cargo transportation.
This could also apply to trade as well, where buying and selling resources can have the player directly dragging resources from their storage to the station's storages, or visa versa. It'd make for a very intuitive resource trading method.
I'd also imagine resources would have different properties. You might have to transport volatile chemicals which are explosive, ore which is very heavy, plant matter which is perishable, and should be transported quickly lest it rot (or be kept frozen using power cells in the process), tanks of rare wares which are fragile and will be damaged by fast acceleration or damage to the hull, and so on.
Speaking of transporting stuff, will there be random events to add some more unexpected occurances to travel? Things like being pulled out of FTL space by pirates, increasing in likelyhood in dangerous sectors, or FTL mechanical failure from poor mantainence or similar?