Remove the tough ends from the asparagus and cut into 2-inch pieces. Slice the zucchini into 1/4-inch thick rounds. Toast the pine nuts in a dry skillet over medium heat for 2-3 minutes, stirring occasionally until fragrant and lightly golden, then set aside. This toasting step deepens their flavor and adds a crucial textural contrast to the finished dish.
Heat 1.5 tbsp olive oil in a large skillet over medium-high heat. Add the asparagus pieces and cook for 5 minutes, then season with salt and pepper. Add the zucchini slices to the same pan and continue cooking until both vegetables are lightly charred and tender, about 4-5 minutes longer. Transfer to a plate and set aside. I like to get good color on the zucchini—it adds a subtle sweetness and depth that raw vegetables won't provide.
Bring a pot of salted water to a boil and cook the spaghetti until just al dente, about 8-9 minutes. Reserve 1/4 cup of the pasta water before draining. While the pasta cooks, heat 2.5 tbsp olive oil in a small pan over low heat. Add the minced garlic and cook gently for about 2 minutes, stirring frequently—the goal is to infuse the oil with garlic flavor without browning it, which would make it bitter.
To the warm garlic oil, add the reserved 1/4 cup pasta water and stir in the nutritional yeast, cooking for about 1 minute to allow the nutritional yeast to fully dissolve and create a creamy sauce. Add the lemon juice, lemon zest, chili flakes, and a pinch of salt and black pepper. Taste and adjust seasoning as needed. This sauce is light but packed with umami from the nutritional yeast and brightness from the lemon.
Add the cooked pasta from Step 3 to the sauce and toss gently to coat evenly. Add the sautéed asparagus and zucchini from Step 2 back to the pan and toss again over low heat for 1-2 minutes to warm everything through and allow flavors to meld. Transfer to a serving dish and top with the toasted pine nuts and fresh mint leaves just before serving. I prefer to add the mint at the very end so it stays bright and aromatic rather than wilting into the warm pasta.