Has an NPB (Japan) game ever ended 12-9?
It has. 12-9 has been a NPB (Japan) final 35 times in 63,173 games. The first was Shochiku Robins beat Yomiuri Giants on May 30, 1950; the latest was Tokyo Yakult Swallows beat Chunichi Dragons on September 4, 2018.
That makes 12-9 the 98th most common final score out of 223 that have ever occurred in NPB (Japan). One point away, 13-9 has happened 24 times and 12-10 has happened 34 times.