I still can't see why crews going through these waters can't be armed.

 

Every navy should deal with those dogs in this fashion.

 

Some shipping companies have begun hiring armed guards for their ships, personally I don't see why they don't spend more for fuel and avoid the area all together.

 

Batman Strategy: "I'm not going to kill you. But, I don't have to save you."

 

Too many legal hurdels.

 

There are certain groups you don't fuck with in this world. (and sometimes i wish we'd be more like them on specific, justifiable occasions.)
the Mossad.
The Russians.
just to name 2.

when dealing with Pirates, it should be simple. Board the ship, kill, dump bodies and let the ship's crew keep on sailing like nothing happened.

and if a pirate boat is captured, leave one body on board with a note:
"you're next, comrade."

let the bosses know they got problems coming.