Preheat oven to 375°. Mix flour, chocolate chips, almonds, and baking powder in a medium bowl.

Whisk coffee and cocoa powder in a large bowl until smooth. Add cinnamon, cloves, nutmeg, and salt and whisk until smooth. Whisk in egg, egg yolk, granulated sugar, oil, and zests.

Stir in dry ingredients with a large spoon until just combined; do not overwork the dough.

Turn dough out onto a work surface. Divide in half, then roll each half into a 1½"-wide log. Flatten to 2" wide. Slice on a bias into 1"-wide cookies. Transfer to parchment-lined rimmed baking sheets, spacing at least 1" apart.

Bake cookies until firm around the edges but still soft in the middle, 8–10 minutes. Let cool.

Do Ahead: Cookies can be made 2 months ahead; store airtight and freeze.

Melt chocolate and butter in a medium heatproof bowl set over a large saucepan of barely simmering water (do not let water touch bowl); stir constantly until chocolate is melted and smooth (you can also do this in the microwave). Whisk in powdered sugar and 5 Tbsp. boiling water until smooth.

Dip tops of cookies into glaze and top with colored sanding sugar or sprinkles. Let cool until glaze is firm, about 2 hours.