The controls in the Default Clock pane of World Clock Deluxe Preferences don't affect existing clocks: World Clock Deluxe uses the default clock format just to set up new clocks.
Choose Pane > Clocks.
Select the clocks and choose Batch Change from the Action pop-up menu (looks like a gear) at the bottom of the list.
To select clocks that are next to each other (contiguous) in the list, press the Shift key and then click the first and last clock; to select clocks that are not next to each other in the list, press the Command key and then click each clock.
Specify a format.