Set up:

• Install ibus and ibus-mozc
• Install terminology
• Configure system to use Japanese mozc input, as well as English
• Add this line to .xinputrc: export ECORE_IMF_MODULE=ibus
• Open a non-EFL application
• Switch to Japanese, and enable Hiragana input

After taking these steps, Japanese input on any other application works. On Terminology (and probably other EFL apps), it keeps writing in English.

If the same steps (the KDE equivalent, at least - needs in-config to be run first) are followed on a Debian unstable system, Japanese input works.