Whaling sucks. You can't do it without cheesing, and it carries a ton of risks (on top of potential death), and the reward you get from doing it is incredibly OP. But whaling will probably never work with the current combat system- unless..
Unless ship combat on its own was an entirely different form of regular combat!
The idea is simple: While on a ship, you don't engage in regular combat. Instead, you engage in 'ship' combat; the primary actor here is whoever is driving the ship, but crewmembers should have some sort of role.
In order to engage in ship combat, you must be piloting a ship. When in ship combat, your entire deck is replaced with a 'ship combat' deck; composed of moves completely different to the current system. These moves should have a much slower pace than regular combat, but I won't get into the details of them because the details don't matter: The idea is that if you're on a ship, you're using completely different stances, manuevers, attacks and defensive options. These options still work on creatures not engaged in ship combat, but suffer a penalty to attack weight when attacking a creature that's neither on water nor on a boat. Certain combat options can only be used if you're on a specific type of ship (which might also pave the way for other ship types that, for example, are specifically intended for war and not travel.)
When in ship combat, creatures on a ship do not directly suffer damage; instead, their ship does. When a ship runs out of health, they are broken down and fall apart, and only then can you target the poor hearthlings that were in it.
Whales would respect ship combat; if they cannot reach their target, they will use a longer ranged attack that deals heavy damage to a ship. Archery maybe also might damage ships, i dunno.
yeah thats it just make a new combat system for whale combat and have ships be the health bar instead of hearthlings. would also solve some issues with ship concerns for murder and whatever