Never checked before or after, if he's wanted I shoot. If the system vessels immediately turn on me I just assume they are naughty mob enforcers in thrall to a pirate and kill him anyway (and them sometimes after the bounty versus fine calculation).
I prefer to role play it as an extra challenge rather than rage about something that might or might not be a bug.
I'm not raging, just avoiding an area of the game that I find to be somewhat illogical and immersion-breaking. I didn't see higher bounties or more targets in Anarchies; if that changed I'd go back.