This is the more malign form of the "British Kitchens!" spambot MO.
The british kitchens spam was link spam, intended to increase the page rank of a target website with google, and other high profile search engines, in order to direct more traffic to their target site.
This is similar, but more nefarious. An invisible link is injected into the source code, but the page-rank engine tracks links between pages. Every time Bay12 is linked, this link is also processed, increasing their score. Because it is so low key, Toady never saw it, and thus never deleted/corrected it.
The purpose here is to not draw attention, and to leave the site completely functional-- while still increasing page rank scores.
Reverting the spam injection stops feeding the spammer, but the underlying problem was that the injection was possible in the first place. If the site runs on a linux or other *nix server (I think it is nginx, so probably.) then I would suggest running the daemon under a user credential that has only read-only access to the HTTP host directory structure. That way any further attacks against nginx would get cockblocked by the host OS's file system security.
I would also look into seeing if there are any updates to nginx. (The version in the maintainer's Repo might be out of date.)
Here is a current list of NGINX vulnerabilities.The thing to remember here-- Don't run a service daemon that interacts with the internet at large with any more access than it absolutely needs to do its job. Should the daemon process be compromised through an exploit, if it is already locked down by the OS, then the hacker can't easily escalate further. NGINX needs write access to its log folder, but that's about it. The SQL back end needs write access to where its database files and log files are stored. Everything else needs to be read only access (system libs, etc..) or forbidden totally (There is no reason for these daemons to see ANYTHING in /dev, for example. Deny even read access there.)