Xah Lee is correct in a way, if you look around for [his] other articles, e.g., on history of Emacs bindings. HHKB is designed for a software environment entirely different from modern systems. If you use just a terminal emulator and Emacs, as they were intended, HHKB might be fine to a certain extent.
The point is, you can do much better than ANSI HHKB or direct Model-M clone. JIS HHKB is one possible step in that direction.