When you loaded the page you got the state of each of the one million checkboxes. That's the data. People just wrote computer code to read that. You can also check a box to write, manually or with computer code. So you can read and write. Usually you talk to a database with a language like sql but in this case, checkboxes work too ;)
Once you have the data, folks just tried looking at it in different ways to see what was there.
I guess the question might be more along the lines of... Does JavaScript watch each checkbox and POST to some URL when the local user toggles one? Does it poll some URL to learn about changes from the server? Maybe web sockets?
The author has another post that describes how the website worked, including how it changed over the course of its existence. But briefly, yes, web sockets are used to stream updates from the server.
Once you have the data, folks just tried looking at it in different ways to see what was there.