I don't know that this applies to sand. Lots of folks here use sand as a component of their substrate to great effect. ...
What can sometimes "poison" a tank is if there is a space where "anerobic" (without oxygen) bacteria growth can take place. There are both "good" and "bad" bacteria than can only survive in a place with no oxygen. I don't remember the names of the organisms.
One "good" anerobic bacteria is a species people without planted tanks try to cultivate in an apparatus called a "denitrator". Many people have had horrid experiences with these devices - others think they're wonderful. Denitrators try to make anerobic conditions in a very slow flow of water from the tank to grow this "good" bacteria. This little guy processes nitrate into nitrogen gas - removing nitrate from the aquarium. A much simpler way to remove nitrate from the aquarium is to do partial water changes.
A "bad" anerobic bacteria makes the "rotten egg" smelling gas that can poison a tank.
Both can grow in an anerobic environment.
I suspect the "stir the sand" recommendation is to get oxygenated water all through the substrate again, to prevent having anerobic conditions down in the substrate.
What you want is a very small circulation of water in the substrate to help keep a little oxygen down in there.
Some of the guys who use sand in their tanks can tell you what kind they use and what their experiences have been.