Some haunts it seems can be defeated with weapons are magic such as the "Chamber of Screams" which is defeated by destroying chains. There is no obvious way for a player or PC to know how to get rid of these haunts. Is there supposed to be a knowledge check involved, and if so would it be arcana or religion?
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They're fairly explicitly undead:
The distinction between a trap and an undead creature blurs when you introduce a haunt—a hazardous region created by unquiet spirits
As such Knowledge (religion) should give information about them. I have the impression haunts vary greatly from instance to instance and are meant to be difficult to figure out, so maybe the DC should be 15 + CR as a rare or obscure subject.
Just as a random thought, Sense Motive might also be appropriate.