Here is why the S-boots were better at sea than the MTBs - the Lurssen Effect
OK, basically, the center rudder did all the steering and behaved exactly like a normal single-rudder set up, so the S-boats were, in effect, single-rudder ships.
The two outboard rudders were 'trim rudders', designed not to assist with steering, but to affect the angle of the hull as it goes through the water.
At low speed, the two outer rudders would remain parallel to the line of travel. Once the vessel got up to about 25-26 knots, they would be turned outward, away from each other, until they were pointed 30-degrees out from the line of travel. This caused the water to be pushed ahead of them, instead of passing cleanly around them. Because this zone of water traveled along with the hull, the screws were kept in a zone of water that was moving more slowly past them than the actual speed of the ship. The propulsive force of the screws is increased, allowing them to push the vessel along at a slightly higher speed (about 1 knot) without increasing RPMs; basically, instead of spinning the screws faster to keep up with the water rushing by, you have slowed the water down to allow the screw to push against it at the same RPM.
The biggest benefit is that the stern of the vessel gots pushed upward, leveling the boat, which eliminates the 'rooster tail' stern-wave and also cuts down on drag. The rising stern forces the bow back down, and the 'white water' bow wave disappears. So now you are going 27 knots instead of 26, making less noise, and showing very little wake.
Of course, you want to go faster than 27 knots, but the drag of the trim rudders angled out 30 degrees prevents this. But here is the cool thing...once the Lürssen effect kicks in, you can slowly bring the trim rudders back towards the centerline as you increase speed, without disrupting the effect, until they are at just a 17-degree outward angle. Now the speed increase is on the order of 5%, so you can go 42-43 knots on the RPM for 40 knots, and you are still making very little 'white water' wake. So you have no white-water wake to betray your presence at night, and you are making less noise than you enemy...does it get any better for a night attack?
From this site
http://p216.ezboard.com/fwarships1discussionboardsfrm14.showMessage?index=11&topicID=1032.topic
The Lurssen effect also gave better acceleration and the single centre rudder and two aerofoil shaped outer rudders gave better maneuvrability than the MTBs
Because the S boot was quite level even when speeding at sea, a Luftwaffe gun turret could be placed in the nose, with 360 rotation and 90 elevation without the bow of the Sboot pitching up and blocking the view like on MTBs
Bow 2cm gun
4cm Bfors salvaged from an Sboot
From
http://www.prinzeugen.com/Weapons.htm