I can see the adjustment for mouse, but not for gamepad.
I'm running the latest version on Ubuntu 17.04. Downloaded the .zip.
Since most people play this game with mouse and keyboard, there is no settings GUI for gamepads. You need to change these settings with the ingame console (shift+esc to open it).
You can search for the right cvars with "apropos <searchterm>", so in your case "apropos joy".
Also, it seems like the default gamepad mapping for Linux is not right as seen here:
https://gitlab.com/xonotic/xonotic-data....ssues/1947
