The polycarbonate is covered with a thin film to slow the clouding/yellowing that raw polycarbonate gets. You have to be gentle when wiping them, especially if dust is on the cloth or polycarb. Presumably this is something to do with blocking UV but I'm not sure and haven't looked into it.
Basically treat them the same as plastic eyeglass lenses that also usually have films (e.g. anti reflection films).
If you damage the film, you'll just have more scratches, unevenness and potential for clouding or yellowing all of which are treatable; just that if you're careful then you won't have to treat it.
As a poster above said, you can't avoid rocks, bug guts, birbs, birb poo etc but you can avoid damaging it yourself.