We bought a 17FQ this past summer and I was wondering the same things. Rocks may be the least concern. A friend had a tire disintegrate at highway speed on his travel trailer and it destroyed the black/grey water valves and outlet plumbing. That made for a crappy situation! Don't know how much protection a plastic or rubber mud flap would provide. May look into something beefier.
As for critters I think the mice would love that enclosed area. You might have success with wire mesh but they sure can find their way into the smallest of spaces. Let us know what you come up with.
Barry & Rose
Barry, MSgt, USAF, Ret. & Rose
2017 Ford F150 w/ 3.5 EB
2014 Coachmen Viking 17FQ