That article is very nice but you're not reading it correctly if your takeaway is that "1.1% of users would benefit more from a CSS menu than from a JS menu". GDS is the UK government - a large portion of that 1.1% is likely not loading the CSS either. Bots, crawlers, rss readers, etc. The 0.2% number is much closer to what you're looking for.

And to repeat: Those that disable javascript have a choice in the matter. Accessibility isn't a matter of choice.