As I understand it, the Guardian had previously always considered D-notice requests and had usually acquiesced. However, it decided that Snowden was so important that it took the pretty unprecedented step of ignoring them.

This made the intelligence services particularly dischuffed.

Post-Snowden the status-quo was re-established.

It remains to be seen whether the Guardian would ignore D-notices again, if something else of the magnitude of Snowden came along - I hope it would use its judgement and do so, if necessary. I'm not necessarily against newspapers considering requests from the intelligence service not to publish something for good reason - it can end up with people dying. It's a tough decision an editor has to make.