I know that pirates throughout history have often acted like mercenary companies and even state sactioned mercenary companies. But apart from the really large pirate organisations there were also mercenary organisations that did not partake in acts of piracy

So from my perspective pirates in sins2 and for that matter sins1, are not really pirates. Because they primarily work for factions as mercenaries. 

Pirates should backstab and be active at all times in small groups. Negotiating a pirate organisation to do your bidding should be a perelous affair, one fraught with information leaks and playing both sides. Kidnapping and skullduggery.

From History we do have examples of like I said, basically state sanctioned or civilisations that were pirates. But I do not consider these real pirates.. it must also be remembered that throughout history some merchants have turned pirate when they wanted to and back. Opportunists if you will.

The thing that Sins has going for it with regard to pirates is that they are willing to hire themselves out to all sides. However their ships are always "ork" like versions of human ships. Rather than run down buckets with a lot of customisation to keep them afloat.

It must be said that during the golden age of piracy, pirates when not "privateers" had very small ships suitable for chasing poorly manned merchantmen, not usually warships capable of taking on naval vessels. They change their flag and hide in ports willing to turn a blind eye or camp out on hidden bases usually. 

I am just thinking that it is fun to have "pirates" in game but that they are really mercenaries paid to run organised raids on targets that often have good naval defences or fortifications. Rather than pirates avoiding combat and going for soft targets.

Food for thought. Bounty Hunters are usually after very specific targets, pirates are usually after soft targets of opportunity, mercenaries are usually private armies anybody can hire to carry out military operations of all kinds. ]

I guess my point is maybe pirate AI should be a little more skittish and able to be paid off or redirected. Using them should have huge risk behind it. Perhaps the pirates even tell who hired them. Maybe they ask for more money after they get their and the target is harder than you told them it was to get to.
Pirates should not be willing to take on your entire navy and defences lightly. They don't get to draw on a civilistation with an organised production and population base that is very large. The risk to them is fairly large.