I also assume that boat will automatically inform authorities and navy/security will be able to reach ship in a matter of hours. With no hostages on container ship, security can just blow up fishing boat/speed boat pirates used and then wait until they run out of food/water on a container ship. Pirates won't be able to control engine/rudder so there is not much they can do other than to surrender.
That might be by exploiting vulnerabilities in the communications and navigation systems, or could be as simple as jamming communications and disabling the vessel by other means. Or hacking the upstream waybill system to direct contents to the port or destination of your preference (already a hacking option with containerized freight). Social engineering (password / token disclosure, bribery) is another option.
Not to mention the fact that pirates seem to want to steal the whole ship and appear to be ill-equipped to offload cargo.
Some especially attentive news watchers may be aware that a large commercial airliner is though to have been lost without a trace in the recent past.
http://www.cnn.com/2013/02/08/world/asia/asia-piracy/index.h...
Then again, they could just be floating fortresses. Perhaps if it takes long enough to steal cargo aerial support could intervene.