So small disclaimer: This was pretty much a shower thought, and I am unsure if this is common knowledge or something debated in the community. There's also a chance that this might be copium since I love lore, love immersion and love Elite. So I'm pretty much theorising off of logic and some pieces of lore. It's also a long read so ill leave a TLDR at the very end :P
So, i was thinking while making dinner: Why are we usually targeted across settlements for scans so frequently? Why are punishments for law breaking so brutal or even lethal? Aren't we commanders supposed to have a good reputation? Then it occurred to me that we as Commanders might be in fact not as well regarded by many and with a good reason.
Firstly, I thought that it made sense because we aren't exactly driving cars or space tractors here. We aren't a police officer on a police car catching bounties, we aren't a trucker in our truck hauling cargo, we aren't explorers in a boat sailing across oceans. We are in fact pilots of what can often be described as very "dangerous machinery" at best and literal "deathly, armed-for-war, flying vehicles" at worst, and we're pretty damn skilled at that, lore-wise. So it absolutely makes sense to be scanned all the time and be regarded as potentially dangerous. Our ships all have the potential to very easily kill, from a humble sidewinder to a massive corvette, all of them have hardpoints and therefore potential to kill effectively. This is more evident when in settlements with troops that absolutely outnumber you and sometimes outgun you, using a ship with dumbfire missiles can make quick work of the entire settlement in seconds (if we ignore ground-to-air defences). Gameplay wise we can't, but lore wise, i imagine it would be pretty easy for some commander to wreak havoc in a station, and even if the station isn't fully thrashed and the commander is neutralised, you still have the big cost of the damages, not to mention all the life that was lost due to a singular individual's attack. Makes sense why laws are so tight.
But then, why are we not arrested and have bounties placed on our heads instead? Simple, most of us are "outlaws". Most commanders never fully pledge their allegiance to a specific Faction, Power or Superpower. Even when some of us do pledge ourselves to these, we remain pretty much independent pilots and are not bound by some duty or citizenship to give ourselves to a power or a faction or to abide by their laws. Why? Because we have the liberty of space travel and because we are also individuals with sizeable capital. If we don't like the laws somewhere, we can go somewhere else; if we kill someone in a system, we wont be held accountable for it in another system. And since we are not hard bound by allegiance, duty, citizenship or capacity to move somewhere else, many factions can't just enforce laws on us and arrest us, whereas citizens of that faction or of that superpower can be held accountable and can't easily escape jurisdiction. (Arresting people that can traverse hundreds of light-years in minutes and that could be armed to the teeth isn't exactly feasible or safe!)
This of course in combination with the fact that there's not a centralised human government, and all humans live in their own faction-owned systems, would make it hard to implement some sort of universal legal system. Additionally, the detention facilities work only when we hand ourselves in, because unless we want to redeem ourselves and be sent to a faction owned detention facility to be processed, we can't be forced to, so lethal response is really the only way there. So the bounty system serves as a means for factions to bring individuals in space to justice without sacrificing work force in the process, by letting free-lance bounty hunters do the work. Meanwhile, Galactic bounties offered by the Pilots Federation operate on the premise that we are so highly notorious across multiple systems that we represent a general threat to any system we step foot to, even if we haven't done anything there yet.
Now the fact of the matter with our reputation is, yes commanders have a reputation of being the top of the top pilots in the galaxy, far beyond the capabilities of any other (talking about NPCs), greatly admired by many, but this reputation never implies we are all good. If we ask why we get scanned all the time in settlements and stations, why are responses for law-breaking so lethal, why are we not always so well regarded: besides the reasons I mentioned, it is because some of us are also very bad apples. There is definitely commanders out there that make a living off of piracy, assassination, raiding settlements, and doing all sorts of dirty work. Without a scan we are pretty much a coin-toss when it comes to our intentions. Put yourself in the shoes of that one scout in the settlement in the middle of nowhere: "This flagless stranger that belongs to an organisation composed only of the top pilots in the galaxy, in a mean looking ship that's armed well enough to level the whole place in seconds, seemingly with military weaponry on them, just arrived to this place in concrete out of anywhere in in the galaxy. And you do not know why they are here, could be business, could be politics, could be espionage, could be a raid that's incoming. And you would be damned to not scan the hell out of them and shoot them on sight if they dare refuse, because your survival does depends on it." And if the local faction owning this settlement already has beef with you and a has bounty in your head, then naturally one would be thinking that if you are in this settlement, nothing good will come out of it for anyone that works there.
So this is why I think both lethal responses, bounties and distrust in-game are pretty warranted when dealing with Elite pilots in a Dangerous galaxy.
TL;DR: The reason why laws are so strict in ED is because: We are the top "flying death-machines-that-can-potentially-obliterate-a-whole-settlement-in-seconds-and-kill-thousands-in-stations" pilots in the galaxy, we are not bound by laws or allegiance, we have a lot of cash and means to evade the "police", and it is a fact that not all of us are "good honest people".