With no humans on board, then there is no incentive not to use deadly force for disabling critical subsystems.
I suspect with drone ships and the lack of crew liability, there will arise contract security companies with pre-positioned ex-seal teams in hotspots to deal with piracy.
It doesn't matter if there aren't any switches or touch screens. Once someone has access to the engine room and steering gear compartment, all bets are off. They can physically adjust valves to get the ship going where they want it to.
Even if they don't have any tools to gain entrance into the ship, they just have to block the air-intakes and the engines will shut down. If it's battery-powered, they just have to let the ship run over some appropriately-sized lines which will get caught in the propellor and seize the shaft.
It's possible to make doors that are extremely hard to cut through... but they can always just cut through the wall instead.
20 lbs of C4 in the control and /or engine room might just do it. So they don't take control (ship can be $urrendered later in pristine condition), they do worse.
So they'll just figure out how to disable the ship. And then they have a big drifting fortress to squat on/ransom/move cargo off of.
A ship without hostages means that a pirate has a good chance of not getting home ever again - the patrols aren't allowed (rightly) to stop a "fisherman" boat in these waters before it's done anything, but once they are on board and making a ransom note, they'd be lucky if they survive to be arrested.
Regarding piracy, autonomy would cut down on costs a lot. Based on my understanding, besides cutting down on life-support costs and having extra room for more cargo, the ships would also be able to eliminate the cost of the armed guards that many have kept on their ships since the rise of piracy. That's one of the main reasons why we don't hear about piracy anymore [0]. With no controls on the ship, pirates wouldn't be able to take control.
Note also that Rolls Royce is looking into drone ships (rather than full autonomy): https://www.rolls-royce.com/media/press-releases/yr-2016/pr-...
[0] http://www.marineinsight.com/marine-piracy-marine/18-anti-pi...