I've always thought that all that sweeping accomplished was to churn up dust, turds, and other crud into the air where you would then be likelier to breathe them in.
It's kind of a non-issue for me as I generally don't stay in shelters anyway, but the way I see it, if a shelter is so dirty that I don't feel good about putting my groundcloth down on the floor and sleeping on it....well if the place is filthy enough that I'm concerned about it, well I probably wouldn't stay there anyway.
Shelters don't need to be swept before use.