I can relate to your worries. I let our teenaged daughters take it out, flip it, swim with the canoe, etc. at last year's Assembly. I was dismayed when they were a little careless when coming back to shore and tracked lots of sand and fine gravel into it, which got between the planks then trapped between the canvas and ribs. This made the hull look highly textured on the outside. I was worried about wear on the tops of the bumps, through the paint and canvas over time.
On further thought, I decided to drum on the canoe to try to get some of that sand to fall out. Some may also work its way out due to vibration when cartopping.
Oh well. It's meant to be used.
I sometimes use the puzzle-edged square pieces of foam as knee pads, but those won't do much to prevent sand from getting between the planking.