iOS 10 Safari JavaScript setting disabled
The following is based on my observation.

By default the Safari JavaScript is enabled, because most of the website that I visited that extensively using JavaScript are working in Safari. The problem starts only when I Clear History and Website Data and go to Settings &gt; Safari &gt; Advanced.

I think as soon as you hit Advanced "for the first time" the program just has an issue as no previous settings are set, thus setting itself to Disable.

I exited from settings and visit the previous website that are using JavaScript, obviously all of them either don't show up or become a Dumb website except you click a link that uses anchor. 

Solution: Just go to Advanced again and set Enable the JavaScript setting. Next time you visit this remain enabled.