Actually I think vaccinating everything even if its only for an hour. When buying in bulk which I am sure the shelters do only costs around $2.00 per dose and is a good ounce of prevention. Some vet clinics even require an animal be vaccinated before doing any work on the animal. A lot can happen as far as diseases go in 72 hours.
There was also a misquote or mistake in that article. HSUS does NOT advocate only keeping animals 72 hours. What they do advocate is not keeping animals that you are not going to put up for adoption longer than the required hold period.
It sounds like very poor management all the way around. How could they have had all those diseases, yet no one noticed dogs were sick & dying? Someone from HSUS had to tell them there was a problem!
Most of the time when a dog comes in the door you have a fair idea who will not be staying - so you don't VX those but IMO all the rest should be. And of course all puppies if they are old enough.