Make the cupcakes: Preheat the oven to 350 degrees F. Line a 12-cup muffin pan with liners. Whisk the flour, cocoa powder, baking soda, cinnamon, allspice and salt in a large bowl. Combine the granulated sugar, milk, vegetable oil, egg, vinegar, red food coloring and vanilla in a blender and blend until smooth. Add to the flour mixture and stir until combined.
Divide the batter among the prepared muffin cups, filling them three-quarters of the way. Bake until the tops of the cupcakes spring back when gently pressed, 20 to 25 minutes. Let cool 5 minutes in the pan, then remove to a rack to cool completely.
Meanwhile, make the frosting: Beat the cream cheese, butter, vanilla and salt in a large bowl with a mixer on medium-high speed until creamy, 2 to 3 minutes. Reduce the speed to medium low; gradually add the confectioners' sugar and beat until smooth. Increase the mixer speed to high and beat until fluffy, about 1 more minute. (If the frosting is too soft, refrigerate a few minutes before using.) Spread the frosting on the cupcakes and dip in the nonpareils; shake off any excess.