Set up the smoker according to the manufacturer's directions. Soak chips in water if necessary (depending on the type of smoking chips used). Lay the thyme branches over the smoking rack to form a bed for the hens to lay on. Set aside.
Season the hens with salt and pepper. In a large saute pan on medium-high heat, heat the olive oil and, when hot, sear the Cornish hens to a golden brown on both sides, about 8 minutes per side. Transfer the hens to the smoker and heat over high heat until smoke begins to escape. Close the smoker completely and smoke the hens until cooked through, about 1 hour. In the same saute pan, add the cipollini onions and cook over medium low heat, turning occasionally, until golden brown on all sides, about 20 minutes. Add 1/2 cup of the apple cider and 1/4 cup of the cider vinegar and 1/4 cup of water and cook until the onions are tender, about 5 minutes. Set aside and keep warm until ready to serve the hens.
While the hens are smoking, make the glaze. In a 3-quart saucepan, render the bacon until crispy. Transfer the bacon to a paper-lined plate to drain and set aside. Discard all but 3 tablespoons of the bacon fat from the pan. To the same pan, add the shallots, garlic and thyme cook until caramelized. Deglaze the pan with the remaining 1 1/2 quarts apple cider and remaining 1/4 cup apple cider vinegar Return the bacon to the pan and cook until the liquid is reduced by half, about 30 minutes. Season with salt and black pepper, to taste, and keep warm until ready to serve the hens.
When the hens are done, serve 1 hen to each guest and garnish each plate with 3 cippolini onions. Drizzle each plate with some of the apple cider glaze and sprinkle with coarse sea salt and a few turns of freshly ground black pepper.