Bring a large pot of salted water to a boil. Cook the pasta until just al dente, stirring occasionally. Reserve 1 cup (240 mL) of pasta water, then drain.
While the pasta is cooking, zest both lemons, dividing the zest into two equal portions. Juice the lemons and combine 5 tablespoons (75 mL) of the juice with 5 tablespoons olive oil, Dijon mustard, salt, and pepper in a jar. Shake or whisk until emulsified.
In a large 12-inch sauté pan, heat 1 ½ tablespoons olive oil over medium heat. Add the shallots and garlic, cooking for 2-3 minutes until the garlic begins to turn golden.
Stir in the red pepper flakes (if using) and cook for another 30 seconds. Add the asparagus and half of the lemon zest, seasoning with salt and pepper. Cook for 3 minutes until tender-crisp.
Reduce heat to low and add the drained pasta, prepared Lemon Sauce, crushed walnuts, nutritional yeast, and ½ cup of pasta water. Toss vigorously to coat the pasta, adding more pasta water if needed for a glossy sauce.
Stir in parsley, basil, the remaining lemon zest, and optional add-ins like capers, olives, or navy beans. Briefly warm everything together for 30-60 seconds.
Serve immediately with a drizzle of olive oil and freshly cracked pepper.