Any warding Charms at the shrine have a minor boon. Shub-Niggurath takes particular care of haunting Shinto believers, perceived personal amusement, she allows the charms to ward of shibito. Cultists through ambiguous means to stay away from them, the cultists believe they can repel and will avoid them, despite there being no effect. The reasoning for this can be inferred or crafted from the DM.
I personally like to think, she wants Shinto believers around to start the next harvest for her and slaughter the cultists once this harvest is over. Shinto is a flexible religion for slipping into with a much wider reach that this town.