As far as I can tell, bumblefoot occurs when staph germs get into a cut on the foot, and the duck's iimmune system cannot get rid of it and so it begins to get encased in a chunky material but the infection progresses anyway. It can really hurt the duck's foot and eventually become a systemic and likely fatal infection. Ooof.
Staph germs (I reckon you know this!) are everywhere, just part of the world. So prevention is pretty much trying to keep ducks from having to walk on sharp, abrasive surfaces. Thorny spots, concrete, asphalt, sharp gravel, wire flooring, can all cut ducks' feet. Strong immune systems can handle many of the germs ducks come into contact with. So keeping them healthy, warm enough, and well rested and reducing stressors in their environment will help, too.
And, of course, spoiling them rotten with attention, bedtime stories, lullabies . . . . that all helps!