1. For the muffins: Place a rack in center of oven and heat to 350 degrees. Grease a 12-cup muffin tin or line with muffin liners. Shred zucchini on the large holes of a box grater (you should have about 2 unpacked cups). Transfer to a clean kitchen towel, gather ends, and twist to wring out liquid.
2. In a large bowl, whisk flours, pie spice, baking powder, baking soda, and salt until combined. In a medium bowl, whisk eggs, brown sugar, oil, honey, and shredded zucchini until combined and creamy; add mixture to dry ingredients and stir just until combined.
3. Fill each muffin cup two-thirds to the top with batter and bake until a toothpick inserted into the center comes out clean, 20 to 25 minutes. Let muffins cool in pan 5 minutes before transferring to a wire rack to cool completely, about 30 minutes.
4. For the frosting: Beat Neufchatel cheese, yogurt, and confectioners' sugar in a large bowl with an electric mixer on medium until thick and creamy, about 2 minutes. Using a butter knife, spread frosting evenly over muffins.