SUMMARY
If you create a new keyboard shortcut that triggers a command, assign it a shortcut (so it appears in ~/.config/kglobalshortcutsrc), delete it, and recreate it, it generates a new .desktop file in ~/.local/share/applications following the naming scheme executable{,-1,-2,-3,...,-n}.desktop.

The curious thing is that the entries in ~/.config/kglobalshortcutsrc do disappear fine when you delete a shortcut, it's just the .desktop file that doesn't.

So if the user keeps testing to figure whether a command works well or not, they might end up with several redundant .desktop files.

STEPS TO REPRODUCE
1. Go to Shortcuts -> Add Command...
2. Create a new command /usr/bin/kdialog --msgbox "Sup"
3. Assign a shortcut to it, for example, Meta+K
4. Click Apply
5. Verify that ~/.config/kglobalshortcutsrc contains a kdialog entry, it should point to kdialog.desktop
6. Delete the shortcut via System Settings
7. Create a new one that also uses kdialog
8. Verify that ~/.config/kglobalshortcutsrc contains a kdialog entry, it should point to kdialog-2.desktop

OBSERVED RESULT
Every time you recreate the shortcut, a new desktop entry gets added to ~/.local/share/applications without removing the original.

EXPECTED RESULT
Every time you delete the shortcut, the original desktop entry gets deleted, and every time you create a new shortcut using the same executable, the new desktop entry reuses its name.