The best way to type in Japanese on Linux in my experience is to use the mozc
input method. It's hidden a little bit in Elementary OS 6, but this is how you can get it working:
Open "System Settings" and go to "Keyboard"
Under "Layout", make sure the left-most list has the keyboard layouts that you have installed. I am using a Japanese keyboard, so only that one is listed.
Under "Input Method", enable IBus (if it has disabled itself again for you)
Click the + button under the list of layouts (on the left-hand side) and filter on "Japanese":
Click on "Japanese — Mozc", then click "Add Engine"
You will now see in the upper-right corner a little widget with a capital letter "A":
This is how you can change your input going forward.
Note: If you do not see the little widget, click "Japanese — Mozc" in the settings or, set the language bar in the upper-right corner.
Open any text editor you wish
Ensure the little Mozc widget is set to the input that you would like:
Give it a test:
When this is all said and done, the Input Method is remembered across reboots. You will not need to reconfigure, reinstall, or rejigger anything.
Note: You may want to also confirm that you have the Japanese language packs fully installed. This will ensure the autocomplete dictionaries are in place as well as a couple of decent fonts. This can be done in the "Language & Region" section of the system settings. Select 日本語 and just hit "Set Language". This will not change the language of Elementary, but will instead confirm that everything has been installed.