95% of the shoulders I've seen in MBN comps do in fact have the skin taken off the shoulder, less what we call the "collar", which is the skin covering the shank bone of the whole shoulder. The collar helps hold the shank bone in place. Without it, there's a good change over the course of the cook the shank bone will fall out of the shoulder due to the meat shrinking down the shank bone as well as the tenderness of the meat surrounding the bone. For presentation purposes you want that shank bone intact and show the judge it pulls out clean. What varies from team to team is the size of a collar left on the shoulder. Some cut it down to just a few inches in width, others leave a large 6 inch or so collar on. Most meat presented to judges comes from the butt anyway, which is on the exact opposite end of the shoulder so that side gives you plenty of bark as it's normally cooked with both the skin and the fat cap off.
That's my two cents. Whole shoulders are awesome, and a ton of fun in my opinion. Hope that helps. You by chance doing Smokin Aces in two weeks at Harrah's Tunica?