For the duck meatballs: Remove the skin from the duck breasts using a sharp chef's knife, and then cut the skin into 1/2-inch strips. Cut the duck breasts into 1-inch chunks, and then transfer to a baking sheet in the freezer for 30 minutes.
Meanwhile, heat a large skillet over medium heat. Cook the duck skin until crispy and most of the fat has been rendered, 14 to 16 minutes, and then remove the skin from the pan and reserve for another use. Pour the rendered fat into a small bowl, leaving about 1 tablespoon in the pan. Add the onions to the skillet and cook until softened, 6 to 8 minutes. Turn off the heat and stir in the breadcrumbs and milk to combine.
Prepare a meat grinder with the finest die. Toss the duck breasts with 1 1/2 teaspoons salt, 1/4 teaspoon pepper, the thyme and juniper. Run the seasoned duck through the meat grinder on medium speed into a large mixing bowl, working in batches. Mix in the reserved onion and breadcrumb mixture and the mustard until just combined, being careful not to over-mix.
Spoon out tablespoonfuls of the duck mixture and roll into 24 meatballs. Place the meatballs onto a small baking sheet and refrigerate for 2 hours or up to overnight.
For the cherry sauce: Heat 1 tablespoon of the reserved duck fat in the same large skillet over medium heat. Add the thyme and shallots and cook until softened, 4 to 6 minutes. Stir in the Kirsch, if using, and frozen cherries along with their juice to combine and bring the mixture to a boil. Continue cooking until the liquid is reduced by half, about 15 minutes, and then lower the heat to medium and whisk in the cherry jam. Simmer for 2 minutes longer, and then season with salt and pepper. Cover and set aside.
Heat 2 tablespoons of the reserved duck fat in a large nonstick skillet over medium heat. Add 12 meatballs to the skillet and cook until lightly browned on all sides, turning frequently, 6 to 8 minutes. Transfer the meatballs to a large plate. Heat another 2 tablespoons of the duck fat in the skillet and repeat with the remaining meatballs. The meatballs may not be cooked fully at this point, but will finish cooking in the cherry sauce.
Bring the cherry sauce back to a simmer, uncovered, over medium heat. Stir in the meatballs to combine and cook until warmed through and glazed with the sauce, 1 to 2 minutes. Serve with spaetzle.
Cook's Note: Crispy duck skin is a terrific snack or can add crunch to a salad or other dish.