I have been enjoying my NY Times subscription for my Kindle DX since last August. I am not aware of any missing articles, perhaps this issue has been fixed.  I do wish the NY Times clipped articles and highlights were available on Amazon website of my highlights.  Perhaps that will change as the NY Times is further along the transition of mixed subscriptions.  For example, they haven't referenced Kindle subscriptions in any of their postings on digitial/online subscription and Kindle readers have been paying much longer than iPad readers.