Fill a large pot with about 9 cups of water and bring it to a boil for the pasta, adding around 1 tablespoon of kosher salt once hot.
Cook the pasta according to package instructions until just tender but still firm, stirring occasionally, then drain while reserving 1 cup of the pasta water.
Zest the lemons and set the zest aside in two separate piles.
Prepare the lemon dressing by vigorously shaking together 5 tablespoons lemon juice, 5 tablespoons olive oil, Dijon mustard, kosher salt, and freshly ground black pepper in a jar or whisking in a bowl until fully combined.
Heat 1 1/2 tablespoons olive oil in a large skillet over medium heat and sauté the shallots and garlic for 2 to 3 minutes, stirring often until the garlic becomes lightly golden.
Add red pepper flakes if using, cooking an additional 30 seconds before stirring in the asparagus slices and half of the lemon zest.
Season with salt and pepper, then cook the asparagus for about 3 minutes until it turns crisp-tender; remove from heat.
Return the hot drained pasta to the pan with the asparagus and pour in the lemon dressing along with toasted walnuts and nutritional yeast.
Pour in 1/2 cup of reserved pasta water and toss vigorously over medium-high heat, shaking the pan and adding more pasta water as needed until the sauce thickens and clings to the noodles.
Stir in the remaining lemon zest, fresh basil, parsley, as well as capers, olives, and white beans if desired, then gently heat for another 30 to 60 seconds.
Season to taste with salt and pepper and drizzle with a bit of extra olive oil before serving immediately.
