Def true. I often mark up math papers and books with DIY-hyperlinks. It's very easy for me to skip over an important, foundational clause just because some term isn't immediately familiar, and if that happens frequently in some reading, then I'm mentally checking out.

For the Napkin book, if the underlying metadata were in the latex source, we could have PDF annotations in a sidebar, e.g., ("def: p.123, key application: p.234, ..."), as well as live tooltips for a modern web experience. That would be totally wonderful for this text and its audience.