There are two trends here.

Many people recognize that it's much cheaper to place nginx in front of other web servers than to buy more servers. We could say that nginx is mainstream now, so any serious website would use it. If you take "top million websites" instead of "top 1000", you might see different percentages. Automated tests just see nginx in the header, although something else is the actual workhorse for the site.

Some of the stuff does not need Apache anymore. As I moved almost all my projects from PHP to Node.js, there's little use for Apache now. And nginx serves static content with less CPU and RAM.