Preheat the oven to 375°F and coat a shallow baking sheet with nonstick spray.
Halve the zucchini lengthwise and, using a melon baller, hollow out each half, leaving a wall of about 1/4-inch on the sides and bottom. Reserve the flesh you removed.
Season the zucchini halves with salt, arrange them on the prepared baking sheet and set aside for 10 minutes to allow some of the moisture to be drawn out.
Blot the zucchini dry with paper towels, then bake until softened, 8 to 10 minutes. Remove from the oven and set aside.
While the zucchini pre-bakes, roughly chop the reserved zucchini flesh.
Heat the butter in a large frying pan over medium heat and add the onion. Sauté until soft and translucent, 4 to 6 minutes.
Add the garlic and continue cooking for 1 minute longer, then add the zucchini.
Season the mixture with salt and pepper and continue cooking until the entire mixture is soft and slightly caramelized, 4 to 5 minutes longer.
Sprinkle with breadcrumbs, 3/4 cup of the shredded cheese and all of the Parmesan. Combine well.
Divide the zucchini-onion mixture between the hollowed "boats," and top each with a sprinkling of the remaining cheese.
Return the zucchini to the oven for an additional 8 to 10 minutes, or until the "boats" are tender when pierced with a knife and the cheese is melted and golden.