The system is clearly designed to take great pains to not lose your data, however whenever you rewrite the core part of the OS that is responsible for booting the system, that is the time when you are most likely to discover a problem:
- Your hard drive or hardware could be flakey and the volume of changes exposes a pre-existing problem that was un-noticed since it was only affecting non-vital files.
- Your unique set of software and settings has a bad effect when migrated to the new OS.
- Your apps you depend upon don't work well yet or ever with the new OS.
- Your command line tools might all get deactivated / moved so it really depends upon which package manager you use and how ready it is to use the new versions of the compiler tools from Yosemite. I would ask a second question with specific details if you want to research that aspect of the upgrade to 10.10.
If you don't have the time to back up fully and have tested your restore process, you might be better doing that and not upgrading to a new OS before upgrading. Or you can check the availability of help to assist in the very unlikely chance you have an issue and pay someone / recruit someone to help you over the bumps.