On Earth, under a 1G gravity field, dust, crap, mites, etc fall to the ground. You can vacuum and clean as much as you want, but the damn stuff gets everywhere. And vehicles like this have lots of nooks and crannies.
Remove gravity, inject lots of shake, rattle, and roll of launch, then orbital maneuvers, all sorts of unexpected bits and pieces will pop up from where you least expected it.
They do this for all Dragon V1 Cargo, and Cygnus visits.
The question would be more interesting, if on a crewed flight, do the vehicle crew wear breathing protection? And when they open the door, do the ISS crew? (I think the answer is no).