If you're worried about tracking, you can block ads and tracking scripts without disabling javascript. If you're worried about viruses, well, all I can say there is that in my experience and understanding, if you keep your browser updated, the odds of getting a virus via browser JS are exceedingly low. Doubly so if you're not frequenting sketchy sites.
I don't know, it seems to me like advice from a time before security was a priority for browser makers, and high-quality ad blockers existed. At this point, I really don't see the value.
Heydon is a developer, and an influencer of developers. He's saying: web development is now absolutely obsessed with JavaScript, and it in no way has to be. The basics, HTML, CSS. That's what's important.