Preheat the oven to 350º. In the bowl of a stand mixer using the paddle attachment, beat the butter and sugar on high speed until light and fluffy, about 3 minutes. Add the eggs and the vanilla and beat on medium-low to incorporate.
In a medium bowl, add the flour, baking powder, salt and cinnamon; whisk just to combine. In a separate bowl or liquid measuring cup, combine the milk and eggnog. Alternate adding the flour mixture (in three batches) and the eggnog mixture (in two batches), starting and ending with the flour mixture; mix on low speed after each addition until just combined. Do not overmix.
Line 24 cupcake cups with paper liners. Using a cookie or ice cream scoop, divide the batter among the cupcake liners; wipe away any batter off the tops of the cups. Bake, rotating the pans once halfway through baking, until the cupcakes have risen and a toothpick or cake tester inserted in the center comes out clean, 18 to 20 minutes. Remove and let cool completely. Can be stored overnight wrapped in plastic wrap before frosting.
Make the frosting: Clean out the mixer bowl, then add the butter and powdered sugar. Beat, starting on low speed and working your way up to high, until incorporated, about 1 minute. Add the eggnog 1 tablespoon at a time, then add the bourbon and sprinkle in the salt; beat until smooth and fluffy, 30 seconds to 1 minute more.
Spread the frosting in a thin layer atop cupcakes. Garnish lightly with ground or grated nutmeg.