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I had never noticed this before. Most of my sites have so many impressions and clicks that I hadn't attempted to add up the line items to see if they matched the totals.
I can confirm that the data doesn't add up for one of my sites. Here is the data for a small site for a piece of software I wrote that isn't very popular. Google Webmaster Tools reports 90 total impressions but only 20 of those are attributed to keywords. Similarly, it says there are 4 clicks, but none of the keywords listed have clicks.
There is little gray "Displaying" text that indicates this.
Unfortunately, there is no way to get additional data out of Google Webmaster Tools. I have confirmed that the export functionality does not report any data that isn't displayed in the table.
This blog post from Google says that the ones that are not displayed are "long tail".
The other change you'll notice is that we're showing a "Displaying" number for Impressions and Clicks. This number represents a total count of the data displayed in the Search Queries table. The number in bold appearing just above it is a total count of all queries including the "long tail" of queries which are not displayed in the Search Queries table.
It doesn't say why they don't display all the data. My guess is that they only tally the clicks on queries fewer than five words long. Longer queries are unlikely to get multiple clicks and impressions. Google omits them to make their database smaller.
For my site the "Top Pages" tab, does add up. All 90 impressions and all 4 clicks can be attributed to specific pages on my site.
It still has the grey "Displaying" text which indicates to me that there may be cases in which they don't attribute all the data to pages on your site. (Maybe if you have really long URLs with lots of parameters?)
