When adding new Keyboard Shortcuts Blender does not check if the shortcut is already defined. The shortcut will be added, but it actually will not be used.
Blender should add some visual clue at least about "Shortcut is already in use". One easy approach could be to disable the text field for the operator-identifier and put a label below the field that states "shortcut conflict, can't assign operator".
Or more visual apparent, add something in red and/or add a warning icon ... Actually anything that indicates a conflict would be better than keep silent :)