For the moment World Cup system doesn't have any logic, it is just an eclectic mix of different competitions. There are a lot of top runners who skip some races or all of them (except WOC, of course). But now famous people in Orienteering - Matthias and Simone Niggli have generated excellent ideas to reanimate IOF World Cup.
Punching at control is an element of action system during O-competitions. Fortunately, now we can see that touch free systems are spread out around the O-world. And I hope that quite soon runners will not care about time lost while punching. But for the moment it is useful to test and improve these skills sometimes.