I agree the risks of immersion to the motor, (especially if it was running) are a big consideration.
The thought had crossed my mind though, from a practical point of view it could fit together quite well.
The engine on my Bernardi fits under the bottom bracket and drives via roller to the rear wheel, and the tank sits on the carrier.
The configuration of the Shuttle Bike wouldn't get in the way, because the roller take off to the flex drive to the prop is also off the back wheel, but higher up. So I guess it would work quite well, using the rear tyre to connect both systems.
Each take-off has it's own tension quick release, so any combination of drive is easy. (engine on land, engine on water, pedal on water, pedal on land etc.)
The Shuttle bike kit was around £700 about 5 years ago, ordered directly from Italy. It is very well made, with nicely engineered and lightweight parts in alloy and stainless steel. The drive is very clever too, a flex shaft from a roller on the rear tyre connects to an outboard style leg suspended below the front wheel, so the whole thing is very maneuverable, and steered with the handlebars just as on land.
They've been around for a long time now, and are surprisingly stable, with some sea crossings that have even been achieved.
The Bernardi engine would put the weight of the motor nice and low. I doubt I'll do it though, I use it on the Norfolk Broads, and the cost of the river license would jump from around £30 to nearly a hundred !