There is definitely an unanswered question as to what the metric, but no, JavaScript is not 90+% by any useful metric. Most code is not a website, and JavaScript penetration outside of the client-side code on a website and some GUI applications on various operating systems is almost nonexistent.

Remember that all of the code in operation includes code like the microcontroller in your mouse, the hundreds of chips in your car doing things like keeping the engine running or "window goes up when I push the button," the DVD menu (which is actually Java code), not to mention all of the staid systems responsible for things like writing your paycheck every other week.

Most of the web is php, so JavaScript isn’t even the primary language on the web.