While it's certainly not a reason to avoid being pirated (just like with Zoners), when it happens, both sides should RP it out. You'd think that would be obvious but...
The one thing that bothers me is when people try to pirate Junkers and immediately go land on Yanagi afterwards. Ok, I only saw something of the sort once, but I think if you pirate someone in a system where their faction has a base, you shouldn't be landing on said base for a while. (Though, again, that isn't Junker-specific)