In a medium saucepan, heat olive oil over medium-low heat and add onion, carrot and garlic. Cook and stir until onion is translucent (5-7 min).
Add tomatoes, oregano, thyme, red pepper flakes, salt and pepper. Raise heat to medium and simmer, stirring occasionally, (10 min), then stir in olives and capers and simmer (10 min). Remove from heat and stir in nutritional yeast. Taste for salt and adjust seasoning.
Meanwhile, heat a large saucepan of water to a boil (add salt and oil if desired), add spaghetti and cook according to package directions. Drain and toss with sauce, then sprinkle servings with additional nutritional yeast, if desired.