Unless you're using second hand (and wet) gravel from another tank its not going to introduce any diseases. Yes sand or gravel requires a little more work than bare bottom, but if your filtration is set up right it shouldn't cause any problems unless you're lazy when it comes to maintanence.
And I'd like to know the meaning of life.
I don't think anyone really knows for sure, although there are a lot of theories floating around I doubt if there have ever been any proper scientific studies done.
My theory is that its mostly to do with genetics and is/can be aggravated by environmental factors. Silvers are the most prone to DE by far, and are also the most heavily captive bred aro and have probably been bred rather unscrupulously because there haven't been any efforts to improve colour [as there is with asians], and also because in a pond environment the drop eye would be minimised. I believe that silvers are more genetically predisposed to it than other aros, and that factors like bright lights above the tank, poor diet, and high tanks can and will make it worse. There is a guy on MFK who has experimented with putting his large silvers in a pond over summer and IIRC he found that the DE improved after the time in the pond. If you compare their natural habitat with an aquarium its not hard to see why, they spend a large part of the year cruising through a flooded forrest with filtered light scanning the branches above the water for food.