Your concerns about the prop clearance over the water are very valid. I can't tell you how many scale PBY's I've seen over the years that simply would not get on the step because the props were sucking up water. I believe you will have the same problem. Give some thought to a solution now, before you go to the trouble of building nacelles and covering everything.
The rule of thumb for float planes is to have 1-2" of clearance above the top of the floats, and the top of the floats in usually 2 or 3" above the surface of the water with the airplane at rest. If the prop gets much closer than that (about 4" above the water), the prop will suck up water.
Possible solutions? Three blade props will help. The deflectors that were mentioned will not solve the problem by themselves because your props are low enough to suck water from directly below the engines. You might try making the nacelles 1 or 2" higher plus adding the deflectors. You could build up the bottom of the hull by adding an inch of styrofoam on the first flight just to make sure it will get off the water. Or add it permanently and skin the bottom with balsa and or fiberglass.
Or hand launch it.