My run has half inch weld mesh under the whole floor, securely wired to the half inch weld mesh sides and top. There's also a little retaining wall with proper foundations round three aides, to terrace the run into a slope, with the mesh fixed behind it. If I thought they weren't perfectly secure in there at night with the pop hole open, I would also be worried about them during the day, especially when dusk falls before they go to roost, as so many fox attacks take place in daytime. When they are out in the garden they are reasonably secure, ie round here so far there have been no problems with foxes, it's more a question of stopping out of control dogs getting in from the field behind. We have fitted a good gate to prevent the dogs, after one incident when luckily I'd just put the girls back in the run, but I expect a fox could get in if and when it found us. Meanwhile I try to balance quality of lifeie letting them out to the grass for a couple of hours a day, and safety, ie providing a run I'm sure nothing could dig or break into. If I'd ever actually seen evidence of foxes in or near the garden I would have to reconsider their time out on the grass.
As for ventilation, I can only say that in all the years I've kept chickens, none of them have ever had any kind of bronchial infections and I put this down partly to luck and obtaining healthy stock in the first place, and also to plenty of fresh air at all times.
Now I'm tempting fate here, aren't I? I expect they will all start sneezing, and the noise will attract a fox!