If there is anywhere something can get in by climbing or slithering through an opening, sooner or later your luck will run out with leaving the pop door open at night. Unless your run is totally enclosed and absolutely no way for anything that digs, climbs, or can get through the bigger openings in the fence or the coop where the hardware cloth isn't applied, leaves your chickens wide open for attack. At night they cannot see and are way more vulnerable and don't have the options of getting out of harm's way like they may in the daylight.
I've got hardware cloth up too but all my chickens are locked in their coops at dusk. I've seen field mice and rats and mink get into the tiniest openings ever!