You can still get to the application form to apply late, but they seem to do some session stuff making the direct link not work (which means you have to acknowledge that you're applying late).

Anyway, go here: http://news.ycombinator.com/apply

Click "apply late". Click "Edit your application online" (number 3).

You should be able to get it at http://news.ycombinator.com/apply . If not, go to http://ycombinator.com/late.html