Disable the default app key (super+num) functionality on Ubuntu 17.10 and later

For Ubuntu 17.10 - 18.10

Run the following command in Terminal:

gsettings set org.gnome.shell.extensions.dash-to-dock hot-keys false

This should disable the default behaviour of Super+0...9.

For Ubuntu 19.04

In addition to Nolf's answer, you can also set these settings on the command line with these commands:

gsettings set org.gnome.shell.extensions.dash-to-dock hot-keys false
gsettings set org.gnome.shell.keybindings switch-to-application-1 []
gsettings set org.gnome.shell.keybindings switch-to-application-2 []
gsettings set org.gnome.shell.keybindings switch-to-application-3 []
gsettings set org.gnome.shell.keybindings switch-to-application-4 []
gsettings set org.gnome.shell.keybindings switch-to-application-5 []
gsettings set org.gnome.shell.keybindings switch-to-application-6 []
gsettings set org.gnome.shell.keybindings switch-to-application-7 []
gsettings set org.gnome.shell.keybindings switch-to-application-8 []
gsettings set org.gnome.shell.keybindings switch-to-application-9 []

For Ubuntu 19.04

Install dconf-editor (sudo apt install dconf-editor) and open dconf-editor. Replace the keyboard shortcuts with empty brackets '[]' as shown in the screenshot.