Its obviously the same gamecode doing it but somehow its sort of less irritating when your criminal buddies turn on you and demand something, after all pirates are a greedy/blood thirsty/backstabbing bunch and might be sorta expected to behave "badly"....same kinda thing might go for the BHG [ex-crims hunting their own, as are many in RL] but yeah its annoying when the Lawfulls do it too....
According to the strategy guide (wut? dar be stretagee gaide 4 freelancer?!?!11!one), being a certain amount of rep with lawful factions mean they won't scan you. I'm guessing this was changed in Discovery, probably because of abuse - smugglers being green with police, etc etc - especially when you already start out on good terms with them.
I'll agree it's annoying when you are scanned by a freindly faction, but it's more annoying when you see someone with say a Outcast ID breezing round Liberty without hostility to the local law. What would be useful was if certain IDs were set to contraband, so for example the police would scan you, find a hostile ID, demand you drop it (obviously impossible) and turn hostile.
Done, NPC's react to IDs. Won't work for freindly IDs, but it would be damn considering players with bugged rep.