Well, some webmasters are seeing more than 999 keywords. I am seeing 999, but Shirsh Agarwal posted a screen shot on Twitter showing that for the first time, he is seeing over 999. He is seeing 1,476 keywords available.
A month ago, we reported that you get a max of 999 keywords listed in your Search Analytics report within the Google Search Console.
Are you able to see more in your Google Search Analytics report within the Google Search Console? Let us know.