Preheat oven to 350º F. Prepare a muffin tin with a thin coating of butter or muffin cups. Mix the flours, sugar, salt, baking soda, and spices together in a large mixing bowl until well blended.
Stir in the carrots and walnuts, then mix in the eggs, butter, and vanilla until all the flour is incorporated. Fold in the blueberries and fill the muffin cups 2/3 full.
Bake for 25-28 minutes until a toothpick inserted in the center comes out clean. Remove from pan and cool on a wire rack.
For the frosting:
In the bowl of a mixer, beat the cream cheese, butter, vanilla, and honey on high for 2-3 minutes, or until smooth. Once the muffins are completely cooled, spread or pipe the frosting on the muffins as desired.
To easily pipe the frosting, transfer it into a zipper-type bag and snip a bottom corner off the bag, about 1/4-inch up from the corner. Pipe frosting by squeezing the frosting out of the hole onto the muffin.
Apply frosting when the muffins are completely cooled. Store at room temperature. If the room is warm and the frosting isn't holding its shape, refrigerate.
Make Ahead: Once muffins have cooled completely, place in a resealable bag and freeze for up to 3 months. Once thawed, top with Cream Cheese Frosting just before serving. Cream Cheese Frosting can be made ahead and stored in the fridge for up to 1 week. Allow to come to room temperature for easier application.