Does upgrading Yosemite risk losing material on HD?
Low as this does get tested before.

What is not tested as much is does each application work with the new OS. Apple can only test major apps it is the responsibility of the App's developer to test their app with the new OS and not all have the time to do this.

But as always with any computer change take backups as there is always a chance of something going wrong.

I assume that changing something will break something else. When it does I have to work out if it is worth living with that problem or revert to the old version.

Another example is professionally in enterprise software when I install a new version of my program I have to provide a tested process that will reverse the change as stopping something working can cost money