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:
What I know we don’t count is the knowledge graph side bar. So if I search for your company name and then it has a link in the sidebar that goes to your company web site as well. So that is something we wouldn’t count in the Search Console. But I think the Sitelinks we should be counting. Otherwise I see that as a bug.
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+.