Preheat the oven to 400°F (200°C) and lightly oil a baking dish.
Wash zucchinis, trim ends and cut each in half lengthwise.
Scoop out the center flesh with a spoon to create boats, leaving about 1/4 inch of flesh.
Chop the reserved zucchini flesh and set aside.
Heat olive oil in a skillet over medium heat; sauté onion until translucent.
Add garlic and cook 30 seconds, then add chopped zucchini flesh and cherry tomatoes; cook until softened.
Stir in oregano, thyme, salt and pepper; remove from heat and mix in half the mozzarella and half the Parmesan.
Fill each zucchini boat evenly with the vegetable-cheese mixture and top with remaining cheeses and breadcrumbs if using.
Place boats in the prepared baking dish, drizzle a little olive oil over them, and bake 25–30 minutes until zucchini is tender and cheese is golden.
Garnish with fresh parsley or basil, let rest 5 minutes, and serve warm.