I can't say whether it's the "proper" way of doing it, but what I have been doing is navigating to /usr/share/applications finding the name of the app and renaming the .desktop file to .desktop.bak (or any name not ending in .desktop), this will make the icon disappear. If you want the icon to re-appear simply return the name to what it was.
Code:
cd /usr/share/applications
sudo mv thunar-settings.desktop{,.bak}