The down thrust has very little effect. If it did there would be a lot of full size boats in trouble. Almost all boats have a down trust unless they use and outboard, stern drive, or have a very deep hull. Just take a look at all the inboard sport boats.
I went this way in the hydro so I could put a larger and faster motor in. The original 3 point hydro's were set up this way, now most use surface props, but the shaft still has an angle to it.
Kap is right a flex drive dose not work well in a scale boat. In reverse the cable can unwind and can also pump water into the boat.
Of my 105 running boats I think that about 85% have the shafts at an angle.
By the way I also fly only 54 aircraft.