I was just looking through the rules and noticed that. My rules-lawyer instincts kicked in.
Rule states that factions at war void the normal rules involving PvP.
Rule states that House factions are at war with the pirates of the same House.
So, yes, if this isn't meant to allow House pirates to attack House traders in cruisers, then the rules needs modified.
And yeah, unless the lawful in a cruiser and the smuggling trader are members of warring factions, the lawful wouldn't be allowed to attack. Again, rules need modified if this isn't what is intended. Of course, there's a Smuggler ID in the new version, so that may clear this up a little bit.
And yes, I'm looking for loopholes. But if I don't find them, someone else will, and they might be interested in exploiting them. And anyway, these aren't actually loopholes, these are things specifically allowed in the rules.