I book through a corporate travel agent and they have some way to add it, but I’m not sure about though JAL’s website. You could try calling if there’s no field for it online.

It does matter since some US airports will make you leave security when transferring and having the number attached to your reservation can get you Precheck when going back though security for the local carrier. Even if it doesn’t print on your boarding pass you issue in Japan, you can stop by the local carrier desk and ask them to print another; then Precheck should be attached. I’ve done this many times.