I would like to give my thoughts on this even though I'm fairly new to the actual mod.
Firstly I would like to state that removing all NPCs is nothing I would like to happen. I did play on German Freeworlds server and they removed all the NPCs there because they made the game crash etc. and the entire place just felt empty as hell.
Yes, NPCs can be very annoying. Yes, NPCs might not help the immersion as much as we would like to but a Universe without them entirely and just Stations is just way too empty to even tempt me to log in anymore.
Furthermore, I saw someone adding the Idea to just remove the Ambient NPCs and keep the patrol route ones. That is kind of the way I would solve this problem if it were my mod. I would scale down the ambient NPC zone to a very limited area (for example in the New York system only Planet New York) or remove it entirely (if that is possible) and only keep NPC patrols near Stations and Tradelanes and that would be it.
This would, in my opinion, add enough "free room" for PvP without NPCs interfering and still have the Universe kinda populated.
It would even make more sense, at least in my head, because why would the Liberty Navy send out a patrol into empty space?
They would rather have them patrolling around an important Tradelane or Station.
Secondly, I would like to comment on the "Should NPCs have CDs" discussion even if it is not the main point here.
I played a mod called Shattered Worlds and even worked with the Devs there. The NPC Patrols there all had 1 fighter equipped with a CD and 3 CD Ammo. That way NPCs could stop you from escaping via cruise speed 3 times (at most if you had no CM) but couldn't CD you indefinitely. It made players pay more attention to what was going on, but it didn't annoy me at all.
I think in conjunction with reduced NPC spawn overall, CDs could add some more flair to NPC patrols (I always feel kinda sorry for NPC pirates disrupting my TL and me just cruising past them as if they didn't know CD launchers existed in the first place), but that is just my point of view.