The sand debate is old as time itself with strong points on either side. Let's look at the cleanliness before anything else. A study done on the bacteria E. Coli showed that bacteria can double every 4 to 20 minutes in optimal conditions. The University of Missouri found, starting with a single germ, that after 30 minutes, there were 4. After an hour, 16. After two hours, 256. After 3, 4096 germs. This was at room temperature. It wasn't specified what germ they were using, and the reproduction rate of every bacteria species is different, but that's a general idea of their growth. This is why completely replacing the sand every week to every four weeks is completely necessary. To spot clean, don't sift the sand, remove all the surrounding sand as quickly as possible to slow the bacteria's growth.
Another big misconception is that sand will without a doubt cause impaction. "Impaction occurs in reptiles when they consume something that they cannot digest. Common causes of impaction are rocks and sand, which might be accidentally consumed when the reptile attacks its prey. Once the substance is ingested it will block the digestive tract and, if untreated, cause death." -Wiki. Symptoms of impaction are, and not limited to, lethargy, lack of appetite, and straining to pass a bowel movement that never comes. While this is every reptile owner's nightmare, it is easily avoided by proper husbandry. A bearded dragon in prime condition that is properly hydrated, has correct temperatures to aid in digestion, and a strong feeding response often won't be affected by sand.
Vita Sand and Calci Sand are fortified with vitamins and calcium that a dragon could eat to bump up their nutrient levels. Though they are sold as "safe" and "edible," they are still very much a danger. The increased levels of intake can still block up your animal.
When used correctly, sand can be safe and very aesthetically pleasing. The best sand to use is silica free children's play sand for a dragon over the age of 1 and is completely healthy inside and out.
E. Coli reproduction - http://www.pnl.gov/science/highlights/highlight.asp?id=879
University of Missouri - http://extension.missouri.edu/fnep/bacterialgrowth.pdf
Impaction - https://en.m.wikipedia.org/wiki/Impaction_(animals)
More on impaction (graphic images) - http://whitney05.hubpages.com/hub/Impaction