I've had the same issue.
To be able to type Japanese in game in Windows 10 the following process works for me.
Install Japanese Ime.
In Win settings, Language, pick the Administrative Language option on the right.
Language for non Unicode programs, the is a button 'Change system locale' in here set Language to Japanese, uncheck the utf-8 beta box. (More on this setting below.
Run the game in windowed mode.
Your now able to input Japanese using the Ime no problem.
(I haven't been able to get typing to work in full screen or virtual full screen modes because I can't access the Ime, maybe someone else has a solution for those modes.
Using this method the Config tool will display '??????????' instead of the proper characters. Turning on the utf-8 beta checkbox will enable the display of proper characters in the Config tool, but you lose the ability to type in game, back to weird garbled characters, until you turn off utf-8 beta.
Ill add pictures and clean this post up when I get home from work.
Hope this helps someone. For myself this was probably the hardest part of being able to start playing the game with confidence.