My guess is if the location is closer to a mountain it's in Tengu territory, and if it's close to a shrine it's Fox territory.
Not all shrines worship foxes. There are many shrines in Japan worship Tengu, too. Tengu can also be servants to other kami and guard their shrines. I have also seen shrines worshipping Tanuki, Mizuchi, or Kappa.
More like the locations are based on prefectures since Japanese from different prefectures worshipping different kami or yokai. Each village also have their own local kami.
BTW, I think the stores that disappeared might be because that the kami lost their power. Kami gains power through their followers and worshippers, but with how many young Japanese don't follow these traditions anymore, minor kami shrines are being abandoned all over Japan.