As for the traders being silent thing, yes, that happens. And yes, it's a bummer.
With regards to your other point, however, there is no reason for the smuggler to force himself to be hostile to the owners of the systems through which he travels. That would indeed be the last thing any smuggler would want to do- to make himself a visibly wanted criminal. The fact that the smuggler is carrying cardi through Order NPC-controlled territory is already covered in RP by the fact that the NPC's can scan and demand contraband. Just because they don't always do the scan doesn't mean that it's OORP to fly past them without guns a-blazin'.
Now, using Omicron-100 is definitely questionable in terms of RP, but that's a separate issue.
