In first site, this song seems to be about mercenaries who fight pirates, but I think it's hidden meaning means the opposite, and it makes the song much more interesting. Many of the ambiguous phrases might suggest it's about the pirates who fight the mercenaries, and some of the unambiguous parts actually support it:
"oceans painted red When the soldiers of fortune hunt for pirates"-clearly it means red because of the blood spilled, but they don't mention WHO's blood-the pirates's or the mercenaries's?
"Slaying a man, taking what you can"-PIRATES take what they can. Mercenaries take what they are payed.
"What is right, what is wrong, who can answer?"-This is actually questioning the existence of moral, while someone serving "the law"(of the empire) would claim that not only moral exists, but he is the moral authority.
"Sailing the seas, we do just what we please"-is exactly how a PIRATE would describe his life
"Scum they are!"-notice the rolling R in the way Mathias sings this line. it's almost like he sings "Scum they Arrrrgh".
"We have no choice, it's you who are the bad guys"-It would be obvious the pirates are "the bad guys", someone who is capturing them won't even bother explaining it.
"You've taken it all"-again, pirates took what they could. Empires took pretty much everything by default. "and yet you still dare to fault"-and yet they blamed the pirates for stealing a relatively insignificant amounts.
"Underneath the paint your flag is still black"-the pirate flag is black with paint, not just underneath it."
"The world has changed, your justice is outdated, What is right, is what is right to me"-again, empire's representatives would claim to be the authority of moral, not trying to change it.
"Share the wealth, your holdings should be ours"- again, the empire owns everything by default, they don't ask anyone to share with them.
"It's all a smile on our sunny bright kolkhoz"-they way that a pirate ship was managed was pretty much like a kolkhoz-almost everyone take part in all of the work except some who were specialists in what they did, and everyone get an equal share of what they got. On the other hand, "kolkhoz" is in no way a word that would describe something related to the empire or it's mercenaries.
"Where's the crime, when no-one's really losing?
Out of cash? Why don't you print some more"-this refers to the more modern empires, who are the only ones who can just "print some more" treasury.
"Emperors, pirates; all cancer"="You and us/Us and you, we are the same and we are both cancer"-An imperialist would never claim that he is as bad as pirate. Also, it is generally common to first mention every one else(the emperors, in this case), than yourself (in this case, pirates).
"Both we are but selfish cancers, Taking what's their"-Someone who speaks for the empire would never say that "we are selfish cancer", or that what the pirates take is their.