A Stormtrooper unit normally has a courage of 1 but within range 3 of Vader it uses Vader’s courage of “-“. Does this mean that the Stormtrooper unit doesn’t receive any suppression tokens or is merely not effected by the ones it has?

You only use the commanders Courage value when checking for panic. All other suppression rules apply normally.

As KingChud said...you assign tokens normally, and they are suppressed, lose an action, etc, as per the rules. They just won't panic. More afraid of Vader than of any rebel scum....