Toss shrimp with red pepper flakes, chives, lemon juice, and salt and pepper to taste. Set aside. In a large skillet, heat olive oil, add garlic and onion, and saute until onion is translucent, about 3 to 5 minutes. Add zucchini, yellow squashes, and dried tomatoes and stir-fly for 2 minutes.
Add shrimp mixture and quickly stir-fry just until shrimp are no longer pink. Keep warm. Bring a large pot of lightly salted water to boil for the pasta and cook pasta according to package directions. Drain. Return to pot and toss with pesto sauce. Serve plates of pasta with shrimp and zucchini mixture on top.