The pirates have small boats, and the ships have big boats. If a machine gun started shooting up a small boat, there's a pretty good chance that it would sink. A big boat won't sink if it's shot up a bit with a machine gun. They could even build a bullet proof area where their security personnel could shoot from so they wouldn't have to worry about getting shot themselves.

I really don't think it would be all that difficult for big ships to defend themselves against these pirates.