Maybe it has all to do with the site itself and the "human" approach Google is taking.
- The site is a non-profit organisation supporting the New York technology community. Domain is .org
- Let's review the page, in all reality such a page is useful - it is showing internet companies made in NYC from a non-profit organisation. What other format would you take? Sure it only has links and looks spammy but it isn't a spam page. It has a purpose and exists in a format that is acceptable by its users - plus, it isn't asking for money. If you were to look at this from a human eye, you would go "this isn't spam"
- Taking the human approach again, if my friend was looking for a collection of internet companies in NYC and he had a research pile with 10 documents and one of them was a handwritten version of this page, shouldn't it be there? Or should it be filed under his research pile of 500 documents? Maybe, we need to see Google differently, it's more complex than a "if statement".
- Maybe reciprocal links to non-profit organisations are viewed differently. A good Samaritan would go "yes" and maybe Google is taking a human approach and going "let me help you as you are a good non-profit organisation"
- Now the nofollow aspect, this is a technical element and I agree, shouldn't it exist? But again, maybe just maybe Google is seeing the site and going "I support such organisations" and the support this can give to other sites isn't so bad.
- Let's take Wikipedia. Would Google punish wikipedia if they didn't have a nofollow? Was the introduction of nofollow done due to Google or a decision Wikipedia made? Maybe it was Wikipedia who noticed users abuse their site and thus introduced the nofollow.
What I'm trying to say is that, maybe Google is evolving to be more complex/human like. It's doing a moral mind on decisions.
On the flip-side, it's just a software that forgot to notice the site amongst the millions of websites out there and in time, it will capture them.