I would think yes, because a prop fully submerged has equal loading at all times on the blades, which would thrust load the propshaft along its axis. The propshaft doesnt care if it is loaded on its axis, thats the loading that it likes. If the prop is run surfaced, then you have uneven loading across the shaft which will impart a moment perpendicular to the axis that is constantly changing each time a blade comes out of the water. That will eventually lead to bearing or propshaft failure.
You are basically bending the propshaft back and forth like you would do a paperclip when you are trying to break it. Its the loading and unloading cycles of blades coming in and out of the water that imparts the moment, not the relative calm of the water, although that wold have an effect too.