I am not a Hetzner customer, but the comment about Nagios perked up my ears. I work with some clients who have Nagios running in their environment, and I'm wondering if there is an exploit in Nagios or if it's just a coincidence that this was where they noticed the infection?
I'm kinda confused about why Nagios was even involved here. If you've got all your checks setup properly, the Nagios host doesn't have any write access to your monitored hosts. You can use NRPE to restrict what commands it runs. Combine that with a read only SNMP account, and even if your Nagios server is compromised it cannot access your server.
It makes me wonder if there's any connection with the recent Drupal Security problem (they cited a "third-party software installed on the Drupal.org server infrastructure" but they haven't - afaik - disclosed the software name yet)
I suspect it's simply out of date. Nagios does have a large surface area, but from what I've seen in the past, monitoring systems are very difficult for sysadmins to want to upgrade. :)
It's most likely that Nagios was simply used as a tool. It's easy enough to add a Nagios plugin that does something naughty and call it check_inode_usage or something.
..not that I'm a fan of Nagios' architecture though. I'm not.