For the sauce: In a small bowl, whisk together the sour cream, lemon zest, lemon juice and salt. Set aside.
For the waffles: Preheat a waffle iron according to the manufacturer's directions.
In a large bowl, whisk together the all-purpose flour, whole-wheat flour, baking powder and salt. Form a well in the center and add the eggs, milk and sour cream. Starting from the inside, whisk together the wet ingredients, slowly incorporating the dry ingredients. When almost fully incorporated, drizzle in the butter and whisk until just combined.
Scoop enough batter into the waffle iron to fill three-quarters of the way. Sprinkle with 1 1/2 teaspoons capers and 1 teaspoon chives. Close and cook until golden brown and crispy, about 5 minutes. Remove the waffle and divide in pieces along the marked lines. Top with a few slices of smoked salmon, a dollop of the lemon sour cream and some chives. Repeat with the remaining ingredients to make more waffles.