what variety are you growing? i grow nabechan which is seed i bought from johnnys. the roots can extend 6-8" below the bulb.
are you planting seed? i grow it in 6 rows per 30" bed. i thin them by harvesting the biggest ones first.

I'm not too sure of the type TBH but I'll be growing from sets.

How deep do you plant them?

Regards
Nick

the only experience i have with sets is for regular onions. when you say japanese onions i think of bunching onions/scallions. when i plant sets i plant them about an inch deep so they are covered.