None of what you said is an inherent problem with JS.
The company I work for has JS app that is resilient against the missing-content problem you refer to. It is also more accessible than any other web app I've ever seen in my life. There's nothing about JS that breaks screen readers: you just... generate the right HTML with the right attributes.
The problems you see with JS apps that don't work are apps written by people who don't care about their app working and don't care about accessibility. That's orthogonal to whether a JS app maintained by a competent team can have better cross-browser compatibility than one (by the same team) that leans entirely on new HTML and CSS features.
The parent commenter is saying that JavaScript in the browser MUST NOT be a dependency for core functionality because it may be disabled ("when JS cannot JS").
If your site is popular over Tor — that is, if it's used for warez or by whistleblowers and journalists who need to browse privately — this may be good advice. If it's not, people who disable a core aspect of the browsing stack are savvy enough to enable JavaScript on a site-by-site basis when necessary.
Well there's our difficulty communicating. I'm talking about all web sites, not just applications that happen to be run in a browser. A regular HTML page with text in it is far more accessible than any application depending on execution could ever be. Web applications can, in very rare cases be made accessible (assuming you have perfect execution and JS feature support in the browser). But actual web pages always are. 99% of the time if you can do it with just HTML and text/images you should.
The company I work for has JS app that is resilient against the missing-content problem you refer to. It is also more accessible than any other web app I've ever seen in my life. There's nothing about JS that breaks screen readers: you just... generate the right HTML with the right attributes.
The problems you see with JS apps that don't work are apps written by people who don't care about their app working and don't care about accessibility. That's orthogonal to whether a JS app maintained by a competent team can have better cross-browser compatibility than one (by the same team) that leans entirely on new HTML and CSS features.