Neat, thanks for noticing, the theme is basically a slightly simplified version of https://github.com/just-the-docs/just-the-docs, never suspected it was an issue with it, I'll take a look to see what can I fix!
I think GitHub Pages only supports a whitelist of plugins, so you might have some more difficulties solving it well without any plugins. I use Netlify for my site, which does support arbitrary plugins.
One quick way to make it faster is to include that "_includes/nav.html" only in a nav.html, and then use an iframe to load that on every page, or something like that.
