As others said, yes, academic papers are still written in LaTex. However, arXiv does not actually accept a pdf for submissions, but require the actual LaTex sources and they generate their own pdf. As LaTex-to-HTML improves, they could always generate it for all of the submissions for which they have the source.
That would be fantastic! I hope it’s on their long term roadmap :). They probably have the biggest corpus of LaTex source in the world, that’d be pretty useful to the project maintainers.
