I recall reading about a really neat ambush that was sprung on them that way, using a disguised "tramp steamer" armed to the teeth, but i don't remember the details, or who pulled it off. I also know that armed helicopters launched from a ship over the horizon were used to spring traps on pirates attacking a "bait" ship. But the problem is expense, it costs a lot of money and time to take out one fast boat with a a few armed men aboard. And there's so many of them, and they're not always there when you're ready for them. It's sort of like using tanks to combat muggers.

Modern navies are just not set up to do this, services like the Coast Guard are more effective, with appropriate equipment, tactics and intimate knowledge of local waters. And if you're successful, they'll just lay low til you leave.