My best guess: The article is about an online faux pas, and hyperlinking to a PDF when an HTML page would be perfectly sufficient is a self-aware nod to another online faux pas. (Fellow HN user oneeyedpigeon points out this faux pas in their comment.)
My seventh-best guess: The NYTimes' CMS lacks support for actual footnotes, so linking to another page is the next best thing. But since the footnote doesn't make complete sense unless you've come from the main article, the web editors didn't want the other page to be easily discoverable. Problem is, the CMS automatically makes any article styled as a regular article SEO-friendly, so they decided to work around that by putting the text into a less-SEO-friendly PDF.
My seventh-best guess: The NYTimes' CMS lacks support for actual footnotes, so linking to another page is the next best thing. But since the footnote doesn't make complete sense unless you've come from the main article, the web editors didn't want the other page to be easily discoverable. Problem is, the CMS automatically makes any article styled as a regular article SEO-friendly, so they decided to work around that by putting the text into a less-SEO-friendly PDF.