proxy_cache / fastcgi_cache the pages output will help. Flood all you want Nginx handles flooding and lots of connections fine your back end is your weakness / bottleneck that is allowing them to be successful in effecting your service.

You could also use the secure_link module to help on your index.php or .html what ever it is you have going on that generates the link they are attacking, You can generate a unique hash that expires for that IP only. There are allot of solutions.

http://www.networkflare.com/