Pirate factions can be at war, all factions can be, and yes if factions are at war hostile trains are subject to attack.
Problem is that people usually use neutral characters for trade that are theoretically not part of the faction. I cannot prohibit this, still if you know for sure that some character is part of faction account there's nothing wrong in attacking this char during a war.
like igiss say's they can buy neutral ID's but my opinion about this is if youre in a faction you need to have a faction tag of it and this is maybe an idea for a server rule???
Greetz Demo
Like the swiftness of the fire death will overcome you