PDF documents have two main benefits. The entire document is a single file, and we know that old documents work.
I regularly read papers from 10 or 20 years ago and sometimes even ones from 30 years ago. The old PDF documents work without any major issues. I have much less confidence that future browsers will continue displaying old HTML documents laid out using then-obsolete techniques in a sane way on future hardware.
What HTML document from 10 or 20 years ago does not still render in a modern browser?
Modern browsers are extremely good to maintaining backwards compatibility at all costs (aka "don't break the web"), to the degree many on HN often argue it hinders evolving web technologies.
I regularly read papers from 10 or 20 years ago and sometimes even ones from 30 years ago. The old PDF documents work without any major issues. I have much less confidence that future browsers will continue displaying old HTML documents laid out using then-obsolete techniques in a sane way on future hardware.