Others have done a good job at critiquing the automated analysis, so I will concentrate on the hypothesis.
>There is a perceived phenomenon among online social news communities (e.g. Digg, reddit) that as the popularity of the community increases, the average member becomes baser and the overall quality of discourse decreases.
I think that's not an accurate portrayal. Having been through the "decline" of Reddit (been reading it even before it had comments!), I observed that the real decline was in the quality(as perceived by me) of stories that made the frontpage(s) and in the quality(as perceived by me) of comments that were upvoted.
In 2006, I would literally read almost every story on the first few pages and the content was very interesting, there were long essays and articles that were on the front page. Now? After the influx of the general public and the juveniles(not saying this in a demeaning manner), quality has dropped in every way. Pun and argumentative threads were the ones that were on top. I do like humor but not just endless pages of snark and humor. Pictures or story-in-headline posts requiring an attention span of 3 seconds tend to get the most votes,
>If a community were suffering from SND, there are a few symptoms we might observe:
>Anxiety, hostility, and depression would rise.
>Confidence, compassion, and happiness would fall.
>The ratios of anxiety/hostility, hostility/compassion, depression/happiness would rise.
>Since each of the negative emotions has an opposite emotion, the last point enables us to measure the general negative/positive trend in each of the three main categories.
How does this analysis address the above points? All the supposed-to-be-funny short comments probably would count as a positive under this analysis. Reddit's community now is pretty happy, confident and compassionate. The analysis is pretty lacking when applied to a supposed-to-be intellectually stimulating social site.
Anyway I see that Slashdot(although not as popular now) and HN seem to have bucked the trend. Although there is some decline on HN, it's not as as steep or as bad as Reddit so far.
Edit: Here's an idea, do your analysis of all the comments of the first x posts of Reddit vs. the same on HN. Could be interesting since they both have almost the exact same format.