Nope, can't say I've heard the "bad bacteria factory" argument....nitrate factory, of course.
The root problem is that gunk - detritus - accumulates.
Now I suppose it may foster lots of bacterial growth to break it down, but this is not "bad bacteria" per se. In fact, without it in our lives we would be in trouble. We buy it in bottles to add to our tanks.
But lots of bacteria (growth fostered by lots of food from detritus) could, in some respect, cause pH problems due to producing a lot of CO2. In tanks that are properly circulated this is not a huge issue, but it can be...it is frequently seen in freshwater systems with less filtration, and with few water changes. It results in a pH drop that actually renders ammonia basically non-toxic. The owners feel a bit of guilts, do a big water change, spike the pH back up, resulting in an ammonia spike taht kills all their fish.
But it is not as common in saltwater due to increased circulation and more water changes.
I suppose people consider those "bad bacteria" but again, I don't. They are no different than the other bacteria really that we rely on to break down waste. It is the waste...and the fact that it is not removed, that causes the problem ultimately, and that is the real source and concern. This is the same argument as the "nitrate factory." It is not the bacteria, but the excess waste, that causes the problems.
Crushed coral needs to be vacuumed because the large pore spaces trap detritus. The angular particles and large sizes also does not foster quite the same infaunal organisms as a sand bed, so those also don't act as well to break down the waste. Additionally, while detritus may stay on the surface of sand, allowing hermits, snails and other "sand sifters" to process it, it can sink rather quickly into crushed coral, so that cleaners can't reach it.
It has its problems, but bad bacteria so far as I am concerned is not one of them. But then, a sand bed can also have bacterial related problems (when anaerobic regions develop, this helps our nitrates, but the byproduct of anaerobic respiration is hydrogen sulfide, a toxic gas, and should a large amount be released, it can kill things).
Crushed coral can work for people, it just may need different care and have limitations in keeping various animals. I don't necessarily believe in telling people "change to sand" because it may not be what they want.
But it is a sink for detritus...and the undergravel filter prevents some of that from being removed during water changes, or cleaned by surface "clean up crew" .
