Is it possible to use joypad instead of mouse in Xonotic?
According to this setting it looks that not.
I need especially the keys for aiming, which I can't find under key bindings.

There are utilities to map inputs to other devices. One of them is qjoypad: http://qjoypad.sourceforge.net/
Discussed xboxdrv in another thread:How can a gamepad control THE mouse?
You can write a simple code run it background in python or C using a library. You need to look an inputmapper library for python or c for linux.
Or you can write mouse driver which get its input from joypad: https://www.linuxjournal.com/article/2476