Who says NPCs won't deliver the same information, if they're a sociable and friendly NPC? You might run into a unsociable NPC that ignores your hails. Guess what? the same thing could happen with a PC! They might feel like ignoring you or they'll give you a canned response. Won't it be awesome when you discover after some responses that you've found a real human from the friendly chat?
I'll probably be playing a "good guy" and will help out when I can. Whether it's an NPC being attacked or an PC being attacked. Won't it be great when after the fight instead of getting a canned "thanks" response you discover you've found a player! You fly to the station together, do some trade routes, form a co-op, get rich, get poor then have a horrible argument and never see each other again! Yay, MP!
The chances of that happening are much reduced if players don't know which other ships are players. Not only that but it will actively discourage interaction between players because the default experience is that there aren't any. It will feel like a single player game and most people will play it as such.
I do like the idea of players being the same as NPCs, but the more I think about it the more it seems like a great idea on paper but a bad one in practice. It's too much of an obstacle to social play for not enough payoff. There's already the solo online and private group modes for people who are OK without social play, and I think it'll be a mistake to bring elements of that into the all group.