Google’s John Mueller confirmed in a Google Hangout on Google+ this past Friday that the Search Analytics report in the Google Search Console does not count impressions and clicks from the Knowledge Graph sidebar.

John said at the 30:35 mark into the video:

He does go into explain more about what is an impression and what is not. I.e. if you have 4 links on the first page, that is not four impressions.

But at least the knowledge graph box is not counted.

Here is the video embed:

Forum discussion at Google+.