The important thing I'm here to tell you is that you need to stop looking under the hood if you want to enjoy this or any other game. Its become common place among gamers to dissect the inner workings and functionality of games, discover the illusions and complain about it. Your ruining your own experience. Stop analyzing and let the illusion trick you.
I like looking under the hood, I want to see an engine in there. Thats what will convince me of a real galaxy, even if I know that its all smoke and mirrors.
Cargo scanning NPCs really shows the lazyness. If I'm in a system with rock bottom superconductor prices, there should be some NPC trade ships leaving with them. Maybe not all, but this is what would be profitable. I know all the npcs are just spawned for my benefit, and I know they aren't actually going anywhere, if I'm not in the system with them they don't continue on travelling on a server somewhere, but while I see them I expect some sort of logical behavior.
If they have illegal goods, they shouldn't dock at a station with no black market.
If the station exports biowaste, they shouldn't bring biowaste to it.
Where are the busted up NPCs returning from a lucky escape. All of them have 100% hulls.
Where are the smuggler npcs that can actually enter a station undetected. I like that there are npcs getting hosed down while docking, but its too often.
These little things add up to making the game world believable or not.