In my experience, there are less non-profits formally working with Holacracy mostly because they can't afford hiring the consultants to help them adopt it. And it's not easy to adopt on your own - it goes against a lot of oft-entrenched habits. That said I know that many have tried, though I don't know how it's going because I'm not even indirectly involved.

Interestingly, the distinction between for- and non-profit is less relevant with Holacracy. The bottom line is effectively the (explicit, written-down) purpose of the organization. More on that here: http://holacracy.org/blog/for-profit-non-profit-for-purpose