Will my files be deleted if I update OS X?
When updating OS X it only updates the system files, so all the files under /Users/ (which includes your home directory) are safe.

However, keeping a regular Time Machine backup is recommended, so that if something goes wrong you can restore your files and settings as needed.

You can go a step further and make a manual copy of your /Users and /Applications folders to a separate disk before installing major OS updates, so you can retrieve them without having to go through the Time Machine interface (for example, on a non-Mac computer, in case you ever need to.)