Potentially you could also establish measures that make it hard for a human to get aboard the ship, such as no walkable spaces, or tall fences, now that you no longer need to accommodate human crew.
Also, an armed rescuing force would have no hostages to worry about.
The other plan would be go on board and reprogram the ship to go elsewhere, the nearest deserted coast say, maybe carry the ship's beacons a ways away in a different direction before dumping them in the sea.
I'm sure if you crash a whole container ship on the coast of Somalia, your confederates could manage to get money out of the contents.
Edit: Also I recall stories of pirates who hacked container companies to actually find where the valuable stuff was. And containers are steel but they aren't designed for any real security.
So if you have successfully hijacked a Pacific container ship full of automobiles bound for Los Angeles... where are you going to dock it? Who does the offloading? And where do you sell 5500 sedans at once that makes all this risk worthwhile?
I think that planting remotely controlled explosives and extorting payment against sinking the cargo is the way to go.
If the transponders are headed to X whilst the ship is headed to Y, it may take you a while before you realise that the ship isn't also headed to X. At which point you now have the problem of determinging which of those fuzzy, cloud-obscured smudges is your ship, and which is someone else's.
Radar can pick up ships, but it also detects, say, rogue shipping containers, of which there are a suprisingly large number.
Existing tracking systems rely on AIS transponders:
http://www.bbc.com/news/science-environment-28372461
Yes, Google can track ships at sea. But it's also relying on AIS, rather than imagery:
http://breakingdefense.com/2012/05/google-satellites-can-tra...
LA-bound cars might be hard. A shipment bound for the Philippines, or India, or elswhere along the Indian or South China seas, quite possibly much easier.
Don't want to suggest automated security systems...too terminator for me at this point.