Blueberries aren't.. The healthiest part of a blueberry muffin would be the blueberries therein. Muffins by definition are not healthy, and making a muffin with blueberries or bran or apples won't magically make the muffin a healthy food. Tasty, yes, but not healthy and fattening.
Yes FlourStoresAsFat. Grinding grains opens all the carbs/sugars within the grain for rapid digestion & absorption, ?es blood glucose more (called glycemic index, Study: http://goo.gl/CiUBvv). Thus all grains, if not eaten totally whole (e.g. everything made from flour=ground grains) ?es glucose>insulin>liver cell removal>conversion to triglyceride fats & obesity. Study: http://goo.gl/uDGIwD, http://goo.gl/C7Ojc4, etc.
Possibly. The blueberries are a tasty addition to muffins but the main ingredients are sugars, fats and eggs which can have a high overall caloric content given the size of the muffin. Consider these in the context of your overall dietary calories especially if your goal is to lose weight.