When you look at motors hanging off the transom of sailboats, you want to make sure the water pick up and prop are in the water. The concern should be if you are anywhere there is alot of wave action and the boat pitch poles for example bringing the prop out of the water, then you may want to consider the longer or 25 inch shaft.
as for the horse power, the max on most transoms are designed up to but no more than 10 hp. In fact with a 9.9, sometimes it may be too much if the bow starts to raise up at or near full throttle as the boat will slow down as it is for easy lack of terms hitting a wall of water because you are a displacement hull, not a plainning hull.
crazy dave