The New York Times built the current site in 2006. The Times just announced that they have are working on a new site design (and presumably completely new architecture) for the last year and should release it soon.
There is a world of difference between doing a cute vanity project that works for say 99% of the time but doesn't mean that they buckle down and do the hard work involved delivering a major publishers site.
Another example Google has a lot of smart people but they cant parse a robots.txt file with a BOM in it.
See http://open.blogs.nytimes.com/ and http://www.nytimes.com/projects/2012/snow-fall/
So they have the skills, but maybe it's for other reasons they don't follow those practices.