Preheat your oven to 400°F (200°C). Line a large baking sheet with parchment paper for easier cleanup.
Prepare the spaghetti squash: Carefully slice the squash in half lengthwise. Scoop out the seeds and stringy bits using a spoon. Place the squash halves cut-side down on a microwave-safe plate and microwave for 5-7 minutes, or until slightly tender. This step helps to soften the squash, making it easier to cut and roast.
Roast the squash: Flip the squash halves so they are cut-side up. Drizzle 1 tablespoon of olive oil inside each half and season with salt and pepper. Place the squash halves cut-side up on one side of the prepared baking sheet. Roast for 30-45 minutes, or until the flesh is tender and easily shreds with a fork. The cooking time will vary depending on the size of your squash.
Prepare the shrimp: While the squash is roasting, in a large mixing bowl, combine the peeled and deveined shrimp with the remaining 2 tablespoons of olive oil, minced garlic, chopped parsley, chives, thyme, lemon zest, salt, pepper, and optional red pepper flakes. Toss well to ensure the shrimp are evenly coated.
Combine and finish: Once the squash is tender, carefully remove it from the oven. Using a fork, scrape the flesh into strands. You can either leave the strands in the squash halves or gently mix them directly on the baking sheet. Add the seasoned shrimp to the empty side of the baking sheet, spreading them out in a single layer. Return the baking sheet to the oven and bake for another 8-10 minutes, or until the shrimp are pink and cooked through, and the squash is perfectly tender.
Serve: Squeeze fresh lemon juice over the entire dish just before serving. Gently toss the shrimp with the spaghetti squash strands. Serve immediately.