It is kind of hard to find, you have to enter through the back entrance to notice it. As you enter there is a cafe on your right and, across from that, a tori (shrine gate) at the foot of a staircase. It is called the Matsutake Jinja as the tori indicates:
Get to the top and behold! The shrine!
Anyway, I thought it looked a little lonely so when I was passing by a few days ago to take these photos I reached into my bag of Famicom carts I had just purchased and fished a random one out:
At least it was for a few seconds, I took the game with me when I left.
This is probably the coolest physical feature of the store. It might seem strange to have a religious structure in a store that sells, among other things, massive loads of porn, but in Japan this is pretty standard. Most factories and other big businesses here actually have a Shinto shrine dedicated somewhere on their property.