In a food processor, combine the pine nuts, lemon juice, garlic, salt, and several grinds of pepper and pulse until well chopped. Add the basil and pulse to combine. With the food processor running, drizzle in the olive oil and pulse until combined. Add the cheese, if using, and briefly pulse to combine. Set aside.

Bring a large pot of salted water to a boil. Prepare the pasta according to the package directions, or until slightly past al dente. Before draining the pasta, scoop up ¾ cup of the starchy pasta water and set aside. Drain the pasta and toss it with a little olive oil so that it doesn’t stick together. Spread the pasta on a baking sheet and let it (and the reserved pasta water) cool to room temperature.

In a large bowl combine the pasta, zucchini, yellow squash, pesto, the reserved pasta water, lemon juice, salt, and pepper and toss. Season to taste. Top with the pine nuts, fresh basil, and red pepper flakes, if using. Serve the salad at room temperature.