you'd need a massive amount of water to cool them down enough
At least, in that circumstance, you're surrounded by the stuff. As you say, it can happen quickly so you'd need a fire alarm and perhaps auto sprinklers. Prob I can see there is a false alarm trashing that part of the cargo.
Since we have 'fridge containers, I'd guess that a container optimised for sea carriage of Lithium batteries could be designed.
I'm happy to pay a little extra for batteries to be assured that there isn't a pallet of them in my pax a/c hold.