Is it an unsafe practice to symlink /etc conf files?

I noticed you add git as a tag--it sounds like /home/ubuntu/etc-config is a git repository with all your configs in it. In which case, it sounds like you're trying to manage configuration files from a central location. If that's the case, I highly recommend looking for a real solution.

Take a look at something like puppet, chef, cfengine, or any of the major configuration manage engines out there. Many of them are free and open source, widely used, and are typically very easy to setup and manage. If you're trying to use a "lightweight" method instead, you'll likely come to regret it later.

If these are on different filesystems, then this is a very bad idea. If the other filesystem does not mount then you will have problems.

I wouldn't use symlinks like this. If you break the link (for any number of reasons) you'll break the config. It's more appropriate to point the server/daemon/app to the actual location of the config file in the init script.

If you just want version control, look at RCS. I've actually found git to be a poor stand-alone server config solution (no locking, no permissions management, the whole directory becomes the repo). If you need something more robust for configuration management, then I'd strongly suggest taking a look at Puppet, Chef, or (gasp) CFEngine.