I don't agree with giving all NPCs weak weapons, it'll just defeat their existence entirely and will result in masses of them attacking each other without any reasonable damage being done.
I haven't really considered this from the perspective of using pirate transports or capital ships, but if I'm in a fighter then I just fly in a circle to avoid their fire. I can quite adequately fight against players whilst having umpteen NPCs attacking me as well. However, if I put myself in a transport, I guess things would change drastically. Even passing through the lanes whilst trading I can lose half of my transport shield to a group of NPCs, which isn't really a problem unless I'm being pirated for real. A pirate doesn't even need to make a demand, they can just disrupt a transport and let the NPCs take it out. I guess that is a problem, now that I think about it.
Now, I've always said that the day NPCs have no purpose in the mod is the day I quit. They're like a living part of the game to me, I interact with them as much as is possible. I recently tricked an LN guy to come to my aid on a lane; I was in no trouble at all, I had 8 Xeno NPCs with me and when the poor sod arrived he lost his shield in a matter of seconds. In any case, he duly blew me up so they didn't really have much of an impact.
But yes, they're quite a problem for transports and maybe that is something which needs to be looked at.