What are pirates going to do with no access to controls?
There will allways be a manual override, on the fancy automated vessels that I check out (fully equiped with Dynamic Positioning systems or DP) there are automatic control systems (DP), simple backup joystick systems and finally simple manual systems (levers for thrusters). These would very likely remain. A pilot would need access to these when taking the vessel into harbour.
Even though it is possible to have vessels remote controlled while at sea they would still need to be manned when they come into the quayside in a harbour. When I come into harbour after testing vessels for sea trials the captain always completes the delicate berthing procedure using the simple manual levers
As for disabling the remote control systems, plastic buckets over the small satellite domes and if there is a large V-Sat then just pull the plug.
So the hijackers just need to come on board the vessel armed with buckets, and perhaps a wire snip for the V-Sat. Also it would seem like a victimless crime to them. They get a ship load of equipment to sell, nobody is hurt, and the insurer pays