If that's the case, then why aren't cargo ships already automated to this extent? It seems like automating a container vessel would be even easier - there are far fewer things to run into on the water (even in a busy port) than there are on a busy highway.

I would bet because the wage paid is insignificant compared to maintenance of the vessel and that the maritime laws would be further complicating such a scenario.

Not so much maintenance as capital costs, I think. Giant cargo vessels can't be replaced as often as trucks either. But drone ships are certainly coming, it's a very trendy topic in the trade publications. I'd give it 10 years.

Pirates? You need a crew on cargo ships regardless of whether they are automated or not.

Crews generally aren't armed to begin with and with no humans to capture and ransom or threaten to change the ships course the amount of booty they could make off with is really limited. Most pirate attacks target hostages anyways. For engineering you could have small crews fly out to any one ship that's experienced engine trouble.