All rudder cables are well clear of the water.
Blowing up the last picture above, you can see one of the rudder lines (highlighted in violet) where it enters the boat and how high it is off the water with Jeff in it. Of course, the stern tends to squat a little bit with speed.

Hobie always enters at the highest point with rudder lines. The opening is small and sleeved with tubes so not a lot of water can squeeze by. Additionally the '08 (as I recall) and newer models have internal 'O' rings in the tubes to seal out the water. Even without the seals not much gets in. I swamp my stern all the time on boat wake rides and end up with a tiny amount (non-sealed versions) as a result.
Here's a close up of the new '09 stern (left) and '07 side by side. You get a better picture of the rudder cable lay out. Also notice here the added hull volume of the '09 as it approaches the stern. From the seam down it has almost twice the depth at the chine. Overall depth of both hulls is the same but the new boat actually sits shallower in the water because of the added volume along the chines.

