Doing nothing on 3 SC bikes with the tunnels and all have been fine.
HT2 is several seasons old and has seen thousands of miles in all conditions and trail types.
Never had a concern or saw the need to try and keep trail debris out of there and a lot of my mileage is in loose/rocky conditions.
However, I maintain my bikes and frequently remove shocks, grease pivots, clean bearings, remove links for cleaning etc.
Haven't seen any damage of note in the tunnels so far...
I'm generally more concerned about rock impact on the downtube just in front of the BB- take a lot of hits there.