As you already discovered, ORK can keep track of certain (ORK-related) game objects via the Scene ID, e.g. to remember collected items or finished battles. They can also be reset via the event system, e.g. to respawn battles after leaving the dungeon or after some time.
For anything else, you can use the Game Object Manager component to manage showing/removing game objects based on variable/quest conditions. There's also a Component Manager to do the same, but just for components.