SEOs and webmasters brace yourselves! Google is now defaulting to the https:// (encrypted) pages even when users are not signed in, with the impact of this being that soon 100% of organic keyword data from Google will be displayed as (not provided). The whole thing has been well illustrated by this graph from http://www.notprovidedcount.com/.
Be aware that no tracking solutions are immune to this change and moving forward, it’s important to devise new reporting logic and methodology in order to keep on top of your SEO campaigns.
One of the solutions you can try is cross reference brand / non-brand data from both Google Webmaster Tools and Google Analytics. Webmaster Tools search query report can provide you with understanding of how people are searching for and arriving on your site via Google, whilst the Bing / Yahoo / Ask keyword data from Google Analytics will provide an accurate representation of how non-Google users are organically arriving on your site.
Obviously such a solution is far from ideal as Google Webmaster Tools is rounded but at least such a process can be replicated on a monthly basis. Still, by combining the two data sets, and also looking into Bing data, you will gain good understanding of how searches are being made across all search engines, and allows us to accurately apportion brand and non-brand visits.
So dear friends – good luck in the new 100% not provided soon age.