Here are another 200 google hits from 2006 to 2016. The tags are often just used for larger features, not every news item.

https://www.google.com/search?q=site:nytimes.com+zapatista&r...

That’s a pretty big gap

I thought so too, but another commenter here found that they were repeatedly reported on during that time, just not tagged as the main subject of the articles. (But maybe this change still does reflect a different level of editorial interest in them during that time.)