I live in West Australia where there are a lot of un-sealed gravel roads, I travel many thousands of kilometers on these sorts of roads every year. Yes the back wheels do kick up a lot of stones particularly with chunky AT tyres on a 4x4.
I have had very little visible damage on my kayak. But I do carry it on the roof rack for seriously rough tracks where I do not want to take a trailer.
On my trailer I have fitted a flat alloy deck which is the material for tray back utilities. This stops a lot of the stones bouncing up.
This is a good lightweight but strong decking that I can walk on while loading without slipping on a slippery boat ramp and ending up with one leg through the trailer chassis. It also gives me a flat trailer to carry other things.
Also I have used shadecloth mesh wrapped over the bow of the boat when carried on my camper trailer. This is quite loose and absorbs the impact of rocks before they hit.