The Pirate: Plague of the Dead [Steam], from developer Home Net Games, looks like it will have a Linux version at launch.
To get the elephant in the room out of the way first, this will be a free to play title with micro-transactions. I'm always really iffy about these sorts of games but their previous game, The Pirate: Caribbean Hunt was exactly the same and is reviewed positively overall. That's a good sign that they might at least know what they're doing.
Feature-wise it sounds pretty packed full of goodies. It will offer a full campaign, an open-world sandbox like experience, a day and night cycle, a weather system along with all the usual features like trading, ship upgrades and so on.
Thanks for the tip HardPenguin!