They dont use "home ports" as base points. They use speed boats that dont need a pier. Most of them set up in random camps along the beach. But that is the small time guys. The top guns doing it run their camps in the city, well under cover with their other scams they run. Like the email 419 network. They just drag their boats up on the beach and cover them up or load them in trucks.
What they do is hijack a ship, move it and the crew off the coast and anchor it. There are ships there that have been in taken mode for months. That includes the crews also.
Its not just going on in the Somali waters, this is also going on in Iran, Pakistan, India too. They are not getting the media on it though and Iran keeps it quiet because its their own people doing it to their own ships.
Best way to handle the problem is to set a example. Just like the other day. Snipe the bastards out.