Position an oven rack in the upper part of the oven and preheat the broiler to high.
Cut the tomatoes crosswise, and pop out the seeds. Season with some of the salt and place cut-side down on a paper towel to drain.
Cook the bacon over medium heat in a large skillet until crispy, about 3 to 4 minutes. Transfer to the paper towel with the tomatoes. Cook the shallot until tender, about 3 minutes. Add the spinach, season with salt, pepper, and nutmeg, stir until heated through and somewhat dry, about 2 minutes. Transfer to a board to cool.
Add the crisp bacon into a bowl and toss with the spinach, cheese, and bread crumbs.
Place the tomato on a foil-lined baking pan, season with pepper and stuff each with some of the spinach stuffing. Broil until warm throughout and tops are brown, about 5 minutes. Serve.