Ah sorry, it should be EST, updated the article to say that :)
For a website with a US centric audience, I think it makes perfect sense to use a US timezone: The graphs match up well with the sleep/wake patterns in the EST timezone. This makes interpreting the data a bit easier, i.e you can easily tell that there is a morning rush, a lunch rush, etc. (although interestingly, the HN audience doesn't seem to have well-defined break hours as there is just one large peak per day).
I'd expect them to match more PST/PDT (-4h), that's where the Silicon Valley and YCombinator are.