I've been away from the hobby for several years, and started a new tank last summer. But I've been at this since the undergravel filter era (1980s).
Over the years, it seemed like disturbing the sand/gravel significantly would always lead to some sort of disease outbreak. I had a tank full of fish that had been healthy for years without any new introductions start dying after a simple tank move from one room to another.
So this time, I didn't vacuum the sand. It's not deep (maybe 1.5 to 2" deep, Carrib-Sea sand).
My water parameters: pH 7.8, nitrate ~ 10ppm, phosphate 4 ppm (very high at the time, now down to .25-.50), no amonia or nitrite.
Just before a strange outbreak without recent introductions, I inadvertently disturbed the sand during a clumsy water change. A week or so later, the fish starting acting sluggish and stressed, with reduced appetite. The royal gramma was flashing/scratching against rocks. I lost 2 clowns and a coral beauty before I saved the remaining two with Metroplex. I still have no idea what the actual parasite or bacteria was--all I know is that Metroplex cured it twice.
I bought a microscope to see if I could identify parasites, etc. (no luck but still fascinating), and I pulled water out of the sand with a turkey baster to check out under the microscope. TONS of critters easily spotted and observed.
So I have read that not vacuuming can lead to disease spread. Pockets of anerobic bacteria can form (not sure why that would be a problem, but ok), some deadly parasites can thrive in there, yada yada yada.
So while my remaining fish were in the hospital/quarantine tank, I left the display tank fallow and started vacuuming the sand every weekend during subsequent water changes (no corals, but had some starfish, snails, shrimp still in the display). The surviving fish are back in the display tank for over a month now following an 8-week fallow period. So far so good.
I recently pulled more water out of the substrate for microscope inspection, and I am finding the population of critters is significantly reduced...it's much harder to find anything swimming/squirming around.
So I guess I am leaning toward regular vacuuming after all of this...if there is uronema in there, for instance, I am thinking a tank can contain it as long as the concentration is minimal.