Use xcape to fix this (KDE users might be interested in ksuperkey). While this small background daemon is useful to bind keys to another (combination of) keys, it also comes along with the feature of running actions only when keys are released, not when they are pressed. Open a terminal and type:
sudo pacman -S xcape
Now you can assign
Super to a placeholder shortcut like ⎈ Shift⎇ Ctrl⇧ Alt
SuperD or any other shortcut that is not taken by another application:
xcape -e 'Super_L=Shift_L|Control_L|Alt_L|Super_L|D'
Make sure to start the whiskermenu with the same shortcut. Do this by adding a shortcut in Settings > Keyboard > Shortcuts. You have to add your xcape command in Settings > Session and Startup > Application Autostart to automatically start xcape when xfce boots up.
Assign
Super to a placeholder shortcut like ⎈ Shift⎇ Ctrl⇧ Alt
SuperD or any other shortcut that is not taken by another application:xcape -e 'Super_L=Shift_L|Control_L|Alt_L|Super_L|D'Make sure to start whiskermenu with the same shortcut. Do this by adding a shortcut in Settings > Keyboard > Shortcuts.
Add your xcape command in Settings > Session and Startup > Application Autostart to automatically start xcape when xfce boots up.