How to disable Cmd + [Num] in Safari
The shortcuts are defined as the first few bookmarks in your Bookmarks Bar. You can see which bookmarks are defined by going to Bookmarks → Favorites Bar. Since they are menu items, you can disable them by remapping them to something else.


Open System Preferences → Keyboard → App Shortcuts.
Click the + to add a new shortcut.
Set the Application to Safari, the Menu Title to the exact name of one of your bookmarks, and the Keyboard Shortcut to something other than ⌘#.


Repeat the process for the other bookmarks.