With helicopters, is normal landing or auto-rotation landing any different when landing on water?
As a helicopter pilot, I've never made a water based landing, so I'm not speaking directly from experience, only from my training, but there are a couple things that are missed in the discussion here that I would certainly worry about.

If I had a real engine failure, and was forced to perform an auto-rotation, in all likelihood, I would not end the auto-rotation with zero forward velocity, I would probably perform a running landing (where you slide on your skids). This, of course, is assuming I'm landing on a flat surface where I'm not likely to roll over (such as a street, parking lot, or runway). Holding the flare to bring the helicopter to a complete standstill has a few risks for me, the biggest one being that if I flare and stop my descent while I still have forward velocity, holding the flare will start to increase my altitude again. Higher inertia (heavier) rotors in small helicopters will suffer from this problem, for example, in training, a Robinson R-22 will generally not have this issue, but an R-44 has much heavier rotors, and we get trained to anticipate a flare at the end of the auto-rotation. Depending on the helicopter, weather, and how I've performed my auto-rotation, if I'm in a real emergency, I would rather put the helicopter down on the ground and slide a little bit than suffer a rotor stall at 50 feet, but a running landing is clearly not an option in a water based landing.

Once I've performed an auto, and the helicopter is on the ground, I'd apply the rotor brake to get the rotors to stop moving before I exited the aircraft, and generally speaking, won't have to worry about the rotors any longer at that point.

If I am performing a water based auto-rotation, there is quite a bit more to worry about. The first thing I have to worry about is that I won't be able to perform a running landing. This means that I'll have less margin for error in my auto-rotation. The second problem is that as soon as I set the helicopter down into the water, it's going to start sinking, and I'll still be strapped in. If I jump out, I'll have to worry about hitting the rotors (or the rotors hitting me) as the helicopter sinks. This means that as soon as I hit the water, I have to remain in the aircraft, and I'll pitch the cyclic over in the opposite direction from the side I'm sitting on, so that I can stop the rotors and still exit the aircraft on the surface side rather than underneath the sinking helicopter. This gets more complicated in the case of passengers, I would encourage them to jump out before the helicopter hits the water, but after my flare, so that they can clear the aircraft and I don't have to worry about them. I only mention it as an additional complication I'd potentially have to deal with.

All of this complexity is a large reason why most of the helicopter pilots I know really do not like flying very far over water. When I'm flying over the water, I tend to stick to an area near the coastline specifically for this reason.