It degrades the immersion in the game. Part of your choice to go and explore 500000LYs away, is that you sacrifice some of the cooler local things in the populated systems. While I myself, give up seeing all the cool distant solarsystems that you get to experience. It's another piece of the game that makes you choose one way or another...sacrifice one thing to get another. I personally like the "one person, one commander" model.
For example... if you want to become a pirate and ruin your good name... it is something you have to calculate before you make that decision. If you had two commander slots, there would be a lot of people playing trader/BHer in one... and a pirate in the other. No thanks.
<puts on flamesuit>
This game/universe have a player with many alter-egos already... in a moment he appears in front of you as a nice trader flying around and just a little later he appears again under the skin of his pirate crazy alter-ego...
The name of his player is "Elite: Dangerous code" (NPC's).
I do not see any difference between this EDC player having the ownership of millions of alter-egos and what is this big problem of real players having a couple of different characters.
For you... you wouldn't see too much difference, because you will find crazy NPC's trying to kill you anyway, regardless if you have valuable cargo or not sometimes.
The difference maybe, is that with more real players doing piracy or crazy assassinations, the space would become "more dangerous" (just remembering the name of the game) and that would be actually more fun, because would make much more sense (and immersive) to fly out there with escorts (and they could add a system to hire escorts of NPC's too, more skilled the NPC hired, higher the price)...
And it's not like this universe is tiny, claustrophobic, making so much difference in the whole that all of us played our crazy alter-egos sometimes... because its actually fun... and crazy alter-egos are in all systems anyway, controlled by the "player one" = EDC.
Besides, you talk about choices, but be a pirate is actually a choice too. People actually can end following a "career" as a pirate and growing their reputation as a pirate. Don't see what difference exists here. You just have to imagine that "it's another person", in the same way that you imagine that the nice trader and the crazy pirate are different, when, technically, they are controlled by the same entity, not a "person", but a machine.
In other words, the game wouldn't change for you, who wants the feeling that you mentioned (you just can ignore the feature, the possibility if you prefer) and the only "change" is that, maybe, more than you get used to, you will have to face more "hard enemies" with more unexpected results, having to think and plan better your trade routes, think better on using escorts, etc.
But the option would add much more richness for many other people, that can never experience some things, due the sacrifice that you mentioned, and instead accepting they end just leaving the game, frustrated.
A totally unnecessary lost of real players (after all, that's the problem with NPC's... they don't buy Expansion Packs or skins), just because you have fear to face crazy assassins, not so "easy" targets as you get used to in your "route" (when, again, the universe already have them anyway).
And would make the universe as a whole richer, but at the same time, not really impacting so much as other games because we are talking about a huge universe here... one that we would have to create one million characters each one and play with all them, at the same time in one million of different computers, and still would seem empty.