Preheat griller. Line a baking dish with foil or baking paper.
Wash zucchini. Cut in half lengthwise, and use a spoon to hollow out the center, reserving the zucchini that scoop out. Season the insides with salt and pepper, and place on the prepared tray.

Heat olive oil in a large skillet over medium-high heat and add mushrooms, the scooped out zucchini insides, onions and garlic. Season well with salt and pepper and let cook until onions get tender, the mushrooms shrink and release their water, about 5 minutes. Add goats cheese. Remove from heat and add thyme and red pepper flakes.

Fill the zucchini boats with the mixture, and top each with a slice of cheese. Place in preheated griller and grill for 7-8 minutes, until heated through, and cheese begins to bubble and golden.