When you open the chest in the room where Shadowheart is trapped on the Nautiloid, it has a couple of mediocre items in it.
But if you take the chest, and remove the visible items in it, you'll notice that it weighs 1 more unit than it is supposed to.
If you carry the chest with you to the beach, suddenly an item in the chest becomes visible that wasn't before: "Pod Key", which looks like, and has the same monetary value as, a Sodalite Shell.
This suggests that either a) there IS a way to free Shadowheart, if you can somehow discover the key before leaving the ship, or b) there's a way to free the woman who gets turned into a Mind Flayer? Have tried a few combinations but no luck yet.