Stir the sour cream, 2 tablespoons dill, and capers together. Season with salt and pepper and set aside for 30 minutes to let the flavors develop.
Preheat the oven to 450°F. Lightly brush the tops of the tortillas with mustard. Place 2 tortillas on an ungreased baking sheet. Sprinkle each with the Monterey Jack, cheddar, onion, remaining dill, and zest, and season with salt and pepper. Stack one tortilla on top of the other, and cover with the remaining tortilla. Bake in the oven until the tortillas are slightly crisp and the cheese has melted, 8 to 10 minutes. Alternatively, you can do this in a covered heavy skillet over medium heat.
Cut the quesadilla in eighths. Top each eighth with salmon, the dill sour cream, and salmon caviar. Serve immediately.