By default, the Cargo Ship replenishes it's loot every 10 minutes - up to 3 times. When the ship docks at the harbor, it will attempt to trigger one of those loot refreshes - although if all three have already happened, it will be unable to spawn any more loot.
The Cargo Ship horn will sound 60 seconds prior to it's departure - once you hear that horn it's time to get moving or you might end up back out at sea.
We think these changes combined will lead to Cargo Ship being a much more contested PvP environment for groups of all sizes. We're also interested to see how a traditionally lower intensity monument like the Harbors adjust to periodic bouts of high intensity action.