I've encountered an NPR for the first time today, only 6 jumps away from Sol. When I first detected their ship with my scout, I just ordered it to burn back to JP and expected it to blow up. Luckily they were friendly and sent me message. After I hastily made a diplo ship, I sent it to their system and we established communications. I guess they don't like me being in their home system, but both our diplo ships are sitting on a JP one jump away and we are increasing our relations. It is now at around 250 and I gave them trade access, just to see what happens, though I don't think they are willing to do the same.
As others mentioned above, it looks like they treat military ships different. I tried to sneak past an intelligence ship to their home system and got detected. They "demanded" that ship to leave the system while they only "suggested" civilian ships to leave, if I remember correctly.
I am a bit confused now though about the active sensor. Based on the alien contact wiki page, I assumed we were supposed to detect a population or an alien ship (not necessarily their diplo ship?) in order to translate their language and establish communications.
For translation checks to happen, both sides must have ships and/or populations in the same system and both sides must be able to detect the other. Detection in this context is Thermal or EM for populations and Active for ships. So you must effectively announce your presence and stay there if you wish to attempt communication (or show the aliens the way to another system for communication attempts).
I also have an active sensor in my diplo ship and they seem to be ok with it.
Thanks, I put active on because passives made it a military vessel, but now I think about it, the NPRs wouldn't know that as they are passive. Shame to loose the no maintenance upkeep of a commercial vessel. Maybe I'll see what happens when I put in my "espionage" diplomatic ship with it's main sensors switched off.
I believe you can put passive sensors on commercial ships as long as they are size 1 or lower.