Heat the oven to 425 degrees. Drizzle squash and shallots with olive oil. Season with salt and pepper. Roast squash cut side up alongside the shallots until very tender, 30 to 35 minutes.
Meanwhile add pancetta to a cold 12-inch high sided skillet or Dutch oven. Cook over medium-low heat until crispy and golden for 5 to 7 minutes. With a slotted spoon, transfer to a paper towel lined plate.
When the squash and shallots are cool enough to touch, scrape out the flesh and slip the shallots from their skins. Transfer to a food processor and add the Bouquet Garni, then pulse together until everything is smooth and puree-like.
Heat olive oil over medium heat, add the garlic, red pepper flakes and the sage and cook until fragrant, about 30 seconds. Add the squash mixture to the pot and stir to combine. Pour in the cream and cook, stirring frequently until it just begins to thicken, about 5 minutes. Add in more FOND if you want the consistency a bit looser.
Meanwhile, heat two tablespoons of olive oil in a non-stick or cast iron pan over medium heat. Add the gnocchi in one layer and cook, flipping once, until golden and crispy, about 4 minutes total.
Ladle soup into bowls and top each with some of the gnocchi and scatter with pancetta and grated parmesan if you like.