The only thing I could find on a quick internet search, including in Japanese, was that none were manufactured that year. I haven't been able to find a reason. Perhaps someone else has more information?
Perhaps due to the spike in silver prices around that time that led many countries to abandon the silver standard?
Fascinating Question. 100 yen silver coins (rice as opposed to 1957& 1958 phoenix motif) were minted between 1959 through 1966. I noted in my JDNA handbook that in 1963 the Japanese Mint released 45MM Silver 100 yen coins. Having studied and worked in very bureaucratic Japan I can only speculate that the necessary permission (signatures - hanko) had not been given. Just prior to 1962, mintage of silver 100 yen coins dropped from 50MM in 1960 to 15MM in 1961. In 1962 Silver according to the records I dug up was selling for $1.60 an ounce on average. The USD purchased Yen 360 (how I miss those days!).