I have a lot of custom shortcuts with scripts and commands that I would like to backup/restore.
I can save other configurations like "customized" icons, application launchers and settings from the home folder but I'm not sure shortcuts are among them.
How are these stored? are they saved in a config file?
They are stored in the dconf system registry in a list stored by the key custom-keybindings under org.gnome.settings-daemon.plugins.media-keys, whereas you have a custom… entry for each custom shortcut (keybinding, command and name), for instance:
TL; DR: so you have to backup the ~/.config/dconf folder
