Preheat oven to 375°F; line a large baking sheet with foil. Cut a small portion off stem end of peppers; reserve tops. Using a paring knife, remove and discard seeds and membrane.
Bring 3 cups water to a boil in a saucepan over medium-high heat. Add barley, cover, reduce heat to medium, and cook until tender, about 10 minutes. Drain well. Spread barley on a baking sheet; let cool completely.
Warm oil in a medium nonstick skillet over medium heat. Add corn and zucchini; cook, without stirring, until slightly tender and browned on 1 side, about 5 minutes. Transfer to a large bowl. Add barley, cheese, salt, lime zest, 1 tablespoon lime juice, 2 tablespoons cilantro, and 1/4 teaspoon cayenne; stir well.
Spoon about 1 1/2 tablespoons corn mixture into each pepper; place peppers on baking sheet. Cover open ends with reserved tops. Bake until tender, about 20 minutes.
Whisk together yogurt, 1/2 tablespoon water, and remaining 1/2 tablespoon lime juice in a small bowl. Drizzle over baked peppers. Sprinkle with remaining 1 tablespoon cilantro and pinch of cayenne.