I used four inch lengths of 3/4" PVC, kind of like pilings. I drilled three 1/4" holes all the way through each piece (6 holes total). My reasoning for the holes was the same--to allow some movement of animals, nutrients, etc. I use three PVC pilings per rock to give three points of support. Frankly, I think using large diameters probably gives better stability--didn't think of it--but I would guess (pure speculation) my method makes for a healthier sandbed, and also allows for more open sand under the rock, if the shape allows for a cave structure or something.
There are several advantages to using PVC supports. The sand under your rock can settle/shift/get dug out, making your rock structure unstable. I think it allows for more interesting structures, both from a stability standpoint and because there doesn't need to be as much rock/sand interface. In other words, it lifts the rock higher off the sand, leaving more sand surface. Instead of having your rock sinking however many inches into your sandbed, just about all your rock is visible, so you end up with more visible rock per pound. If it's gonna be invisible in the sand, I'd rather pay 40 cents for 12" of PVC than $4 per pound for live rock. Among the disavantages are, as you mentioned, probable reductions in animal and water movement.
While Dr. Shimek is almost certainly right about animal movement being restricted, IIRC he made a home for his carpet anemone by sinking a piece of large diameter PVC in his sandbed. I have the highest respect for Dr. Shimek, and I want to be clear that I do not think this is hypocritical on his part, nor am I intending to attack him in any way. In my view (my words, not his), he did the same thing we did; he weighed the advantages and disadvantages of a certain methods, and went with a way he thought would accomplish what he wanted to accomplish.
--Jeff
--Jeff