A possible contribution to the decrease that was not mentioned is that they may be linked to less often because of the pay wall. For general news, a blogger might instead link to some other, more reliably visitable site. When the Montreal Gazette introduced their pay wall at least one blog I follow avoided linking there when there was another source.
Indeed I would think most bloggers would look for alternate sources.
I also find I tend not to follow links if they are identified as NYT, and the loss of the ability to push links to Instapaper has really killed NYT for me.
