the rule is to stick as closely to roleplay ( the generic roleplay of NPCs ) as possible while bending the rules towards your personal role as much as you can while maintaining the general picture of the NPC faction.
in particular that means that a lawful character who defected from faction A can, when its down to his role, indeed bring the equipment with him. - but that means to bend the roleplay of the NPC faction a lot. - NPCs do not leave a faction and join another one. - so NPCs never bring their own possession.
NPCs "think" that the weapons their own faction produces is the very best possible for their needs ( even if we, as players know, that they are rubbish ) - furthermore, a character hardly ever knows the "stats" of a weapon.
now when it comes to weapons. - when you purchase a guardian, you sort of subscribe to the navy, cause its a navy ship. - with the navy comes a contract ( usually the ID ). so now you are flying a navy ship - and have a navy ID. your bounty hunters days are past.
along with the new navy ID comes a responsibility ( in-character ) to represent your new employee. - so ... your character would most probably think its inappropriate to display a full array of pirate crafted weapons. - cause it basicly says "allright, i m in the navy, but your weapons are crap, so i got these ones that happen to be crafted by murderers and criminals, but .... tough luck, they are better weaponsmiths than you are."
cause your char doesn t think that way ( most probably - cause why else would have have gone to the navy ) - he ll try to aquire something that is in line with the lawful weapons of his faction.
but even as a bounty hunter.... he may collect a lot of weapons, - but he ll still think that buckshots / reavers are THE best weapons to counter pirates, cause they are fresh from the developement laboratories and made to hurt the pirates as much as possible.
another argument to drop such weapons is.... once they re damaged, no one in the navy can repair them. - and you won t wanne ask the imprisoned corsair to repair your colada.... .