The Empire referred to the 7th century Japan, not pre-WW2 Japan.
You can find some historical information of Japan in Chinese chronicles. One such record tells us about a situation of Japan (or Wa) in 3rd century, when Japan was divided into more than 100 nations, fighting each other.
Japan was eventually united by Yamato Clan sometimes before 5th century. The king of Yamato Clan then was called OHKIMI or 大王 (Great King), a head of federation of kingdoms within Japan. In the 7th century, the current use of title SUMERAMIKOTO or 天皇 (translated as Emperor) started being used when Yamato Clan try to centralize Japan.
The Emperor of Japan refers to that time when Japan was made up of many kingdoms. And the usage remained till today because the current emperor is a direct descendant of the Great Kings of Yamato Clan, who unified Japan then.
