Stop Dictionary Pop-Up Window
According to Apple documentation Mac keyboard shortcuts  ⌃+⌘+D is built-in document shortcut:

Document shortcuts
The behavior of these shortcuts may vary with the
app you're using.
/.../
Control-Command-D: Show or hide the definition of the selected word.

This shortcut is enabled irrespective whether System Preferences &gt; Keyboard &gt; Shortcuts &gt; Services &gt; Searching &gt; Look up in Dictionary assigned or not.
Keyboard shortcut for 'Look up in Dictionary' will open Dictionary app and not pop up window, so these are different things.
On my machine I observed 'varying behavior' as stated in documentation: I have not assigned shortcut but this key combination opens dictionary pop-up in Mail and Notes but not in Safari. Probably because MacOS doesn't consider webpage as 'document'.