I went to a liquor store to get several bottles of Japanese whiskey as a souvenir, and I was not pleased to be told that each customer is limited to just one bottle.

In Japan, the parties to a contract (seller and buyer) are free to decide what the terms of the contract will be and whether or not to enter into it. There is no problem, basically, if a store decides to sell only a limited quantity of a product. Since it takes many years to mature the original whiskey and production cannot be increased immediately to meet demand, it is possible that the whiskey is sold in limited quantities. You should inquire with the store's staff as to the reason for this.