Sift the flour, 1 teaspoon nutmeg, 1/2 teaspoon cinnamon and the salt into a large bowl. Beat the butter and granulated sugar in a separate large bowl with a mixer on medium-high speed until light and fluffy, 3 to 5 minutes. Beat in the whole egg, egg yolk, the brandy and vanilla. Reduce the mixer speed to low; add the flour mixture in 2 batches and beat until just incorporated. Divide the dough in half, wrap in plastic wrap and refrigerate until firm, 1 hour.
Line 2 baking sheets with parchment paper. Dust each piece of dough with flour and roll out between pieces of parchment to 1/4 inch thick. Refrigerate 15 minutes. Cut into shapes and transfer to the baking sheets. Gather the scraps and refrigerate until firm; reroll once to cut out more cookies. Chill the cutouts 30 minutes.
Position racks in the upper and lower thirds of the oven; preheat to 350 degrees F. Bake the cookies, switching the pans halfway through, until just golden, 11 to 13 minutes. Let cool 5 minutes, then transfer to racks to cool completely.
Make the icing: Beat the confectioners' sugar, meringue powder, the remaining 1/4 teaspoon each cinnamon and nutmeg, and 3 to 4 tablespoons water with a mixer on high speed until smooth and thick. Transfer to a resealable bag and snip a small corner; pipe onto the cookies and decorate with nonpareils. Let set 30 minutes.