My in-laws are convinced that it comes from the 70s, when Japanese chemical warfare on farm bugs (along with pouring pure chemicals into rivers etc) made the common complaints about Chinese imports today seem the nationalistic nonsense that it mainly is. My own theory, though, is that it goes all the way back to Edo times, where the lack of animals (most people never ate meat, milk products were unknown, most people were forbidden to ride horses) meant that the manure was almost always “night soil” (human excrement), with the consequent greater risk of the spread of diseases.
Was about to eat a “normal” sized one for the first time in years and was wondering whether the lack of fibre due to peeling off the skin or the pesticides due to not was going to kill me, and it suddenly occured to me that peeling a small apple is an awful lot more difficult than peeling a nice melon-sized Fuji. Japanese virtually always peel their fruit, if the look of shock on my in-laws’ faces when I ate one without is anything to go by.
The other possible reason that springs to mind is the fact that fruit is often given as a gift in Japan, so the larger, more impressive and more expensive the better- hence also the baskets of fruit that cost three times as much as buying each piece of fruit seperately (the typical Japanese opposite of bulk discount).