Yes, iTunes counts for the charts ... so does amazon, 7digital etc ... in fact, the first "digital-only" single to top the UK single charts did so as long ago as 2006.
However, iTunes has the biggest consumer reach by far... something like 70% of all digital sales go through them... so getting into iTune's own chart (and the resulting visibility around the iTunes site) is pretty useful.
Sadly, it looks like New Noise's impact might've been short-lived - can't see it on the iTunes top sellers page any more this morning