Preheat oven to 450°. Halve each zucchini lengthwise and cut a small slice off the "bottom" so that it sits flat on your surface. Using a spoon, remove the flesh and any seeds from the zucchini. Finely chop the zucchini flesh and set aside.
Slice the pepperoni slices into thin strips and reserve.
Spray the bottom of a baking dish, large enough to hold the zucchini with baking spray or spray oil.
Using a box grater, grate the onion. Finely mince or press the garlic clove. In a medium skillet, heat the olive oil over medium-high heat. Add onion, garlic and zucchini flesh and cook until soft, about 5 minutes.
Transfer zucchini mixture to a medium sized bowl and add the marinara, ricotta, 3/4 cup of mozzarella, 1/2 the zucchini strips, Parmesan, oregano and thyme. Stir well and season with salt and pepper.
Divide the mixture among the zucchini shells. Sprinkle filled zucchini with remaining mozzarella and zucchini slivers. Bake zucchini until golden brown, about 20-25 minutes. If desired, broil zucchini for 2-3 minutes for additional browning.
Garnish zucchini with additional Parmesan and basil slivers, if desired.