According to Rene J. Francillon's
Japanese Aircraft of the Pacific War, In early 1942, the Allied Directorate of Intelligence decided to give unusual yet easy to remember names to Japanese aircraft, to avoid confusion and the use of hard-to-pronounce Japanese names.
Starting with simple "hillbilly" names (one of the staff members was from Tennesee) like Zeke, Nate, Rufe, Jake, and Pete, a system of naming evolved:
Male first names: Fighters
Female first names: Bombers, attack bombers, dive bombers, reconnaissance planes, and flying boats.
Tree names: Trainers
Bird names: Gliders
As with all things in life, there are exceptions to the above. The Nakajima Ki-44 Tojo, for example.
For more in-depth info on Japanese aircraft, I highly recommend Francillon's book. Check it out!