Ever shot from a moving deck? I have - ain't as easy as you might think. Now switch to a high speed small boat, really not easy. Yes, there was at least one encounter with Somali pirates that was stopped by professionals armed with handguns, sorry, disremember, may have been an Israeli security unit.
All of the Somali gear I have seen is in terrible shape, and the reports show that they truly are not match grade marksmen. Shooting rounds into the air or randonly in the streets doesn't make for someone who can take a precision shot off a pitching and bucking Zodiac, or other small boat trying to catch a lumbering whale of a freighter. heck, if they were in a Zodiac it would be easy - pop some shot into that inflatable and watch them get wet.
This doesn't mean they can't get lucky, find spots on the gunwale that might stop a bullet, use cover and concealment as best you can.
One thing that makes me curious, "unwritten policy"? This means if you use your sidearm, and it doesn't go 100% the companies' way, you will be hung out to dry, financially and legally. Get some legal back up in writing first.