Pour water into a baking dish. Place squash halves with cut sides down in baking dish; roast for until tender, 30 to 40 minutes.
While squash is baking, cook and stir ground beef and onions in a skillet over medium-high heat until the beef is crumbly, evenly browned, and no longer pink. Drain and discard any excess grease. Set beef aside.
Heat 1 tablespoon olive oil in a skillet over medium heat; cook and stir mushrooms, zucchini, green and red bell peppers, both amounts of crushed tomatoes, basil, oregano and thyme. Simmer over medium heat until vegetables are cooked through and tender, about 10 minutes. Add the ground beef and onions; stir to combine. Simmer on low heat, stirring occasionally, while you finish preparing spaghetti squash.
Scrape the inside of hot spaghetti squash halves with a fork to shred the squash into strands; divide onto 8 plates. Drizzle each serving of spaghetti squash with 1 tablespoon extra-virgin olive oil and top each serving with a generous amount of meat sauce.