It costs money to arm a ship, or to put mercenaries aboard. And most of the time nothing happens, so the money spent will be perceived as having been wasted. It is easy to think of these ships as being run by massive, super-rich corporations, but very often they are shoestring operations sailing under flags of convenience, with navigation officers from one country, engineers from another, and deck hands from a third, with only of handful of key men to translate orders. It's a very competitive, cutthroat business. They often don't have proper training, safety gear, financial backing, insurance, you name it. These are the Mexican truckers of the high seas. It's not likely any extraordinary effort or expense will be taken to protect them by their owners.

There are many things which could be done, like instituting a convoy system so men-of-war could protect the ships, or an office for filing "float plans" so bad guys could be identified, and so on. But this is expensive, and nations don't want to bother to cooperate to do it. Operating even a destroyer is very expensive for even the world's biggest navies, especially in remote waters far from that nation's interests and where there are no support facilities or bases. Further, modern warships are very poorly equipped for this kind of patrolling. Even a destroyer can cost close to a B$, and putting .50s on it to hunt speedboats on the other side of the world is not an efficient use of resources. Tomahawk missles and Aegis radars are useless in this kind of work, and many modern warships have neither weapons nor sensors optimized for taking on speedboats armed with small arms. Even naval cannon and fire control systems are ineffective against small craft. When modern navies finally overcome their inertia and do something, as they did in Indonesia, the pirates simply stop and they pop up somewhere else.

The situation is really no different than it was several hundred years ago, until foreign navies cooperate, develop bases in remote areas, and design ships specifically for this type of work, the flies will always have the advantage over the swatters. Piracy has always taken advantage of this, and most nations, even going back to the Romans, find it cheaper to pay tribute than to go on the offensive. Right now, several nations are patrolling these waters, and sometimes they get lucky and blow up or capture a pirate, but as long as the chances of success are good, there will always be replacements. And of course, if they make a mistake and hit an innocent target, they get into all kinds of trouble.

I know it sems frustrating and infuriating, but that is one of the lessons of the modern world, sometimes money and technology are useless. And there are always clever and unscrupulous people who will take advantage of that. Just think of porn merchants, spammers and hackers...