Looks like she's missing the high string on the low E. She plays that string a lot. My guess would be that she wants the bass note to provide a foundation without any double string 'shimmer'.
I looked again carefully, and if you watch the video full-screen and look from 0:45 to 0:55, you'll see that she has all 12 strings.
I'm not well versed with 12-string guitars, but it looks like the high string on the low E is really thin, and the high string on the low A is actually thicker.
But that is a captivating-sounding guitar, and well-played at that!