Has an NPB (Japan) game ever ended 16-3?
It has. 16-3 has been a NPB (Japan) final 20 times in 63,173 games. The first was Hankyu Braves beat Nankai Hawks on May 17, 1950; the latest was Tohoku Rakuten Golden Eagles beat Hokkaido Nippon-Ham Fighters on July 15, 2024.
That makes 16-3 the 117th most common final score out of 223 that have ever occurred in NPB (Japan). One point away, 17-3 has happened 22 times and 16-4 has happened 23 times.