Because engines are impossible to disable, GPS is impossible to spoof, and control systems are impossible to hack even with unlimited physical access.
> no crew to hold hostage
There's a fancy robotic ship and a bunch of cargo to hold hostage.
> the practical amount of looting is a fraction of one container
How do you reckon? I suppose if the value-density of the cargo were low enough then nobody would have incentive to steal it, so they would have to threaten to destroy it instead.
> The real objections should be about failure modes of ships and what a crew can to to mitigate them.
You're absolutely right. But piracy is one of those failure modes.