On the planes that I plan to use for floats in addition to wheels I normally mount the rudder servo at the rear of the fuse so that I can then attach a flexible control rod (Gold-n-Rod) to the floats for a water rudder. The only thing to watch out for, as has been mentioned previously, is to put silicone sealant around the servo to keep water out of the fuse. See photo of Balsa USA Stingray for clarification.

On my 80" Midwest Extra 300S, I have the rudder servo inside the fuse and the water rudder is controlled by a servo that's on top of one of the floats, and this hasn't been a problem either for that servo or the two elevator servos that are externally mounted.

In the attached photo of the Extra you can easily see the rear-mounted elevator servos. If you look closely you can also see the port to which the water rudder servo wire attaches, between the cockpit and the wing, and if you look VERY closely you may be able to see the water rudder servo arm (white) sticking up above the rear portion of the left float, behind the rear float mounting bracket.