Grate the zucchini, shallot, and garlic cloves using the large hole side of a box grater on a towel or cheesecloth.
Squeeze the excess water from the zucchini over a sink or bowl until there is approximately ⅔ cup of liquid or more. Discard the water.
In a large pot, boil water and 1 teaspoon salt to cook the noodles.
While the water is heating up, blend the plant milk, flour, and nutritional yeast, and set aside.
While the noodles are cooking, in a large skillet, cook the zucchini, shallot, and garlic mixture on medium-low heat. If the mixture sticks, add a small amount of vegetable broth to the pan.
Cook the zucchini mixture for 5-10 minutes until heated through.
Before draining the pasta, remove 1 cup of pasta water and set aside.
Drain pasta in a colander in the sink. Then, return the drained pasta to the pan and place it on the stove at medium-low temperature.
Add the cooked zucchini mixture to the pan with the pasta, add ½ cup of the pasta water, and toss the pasta and zucchini mixture together using tongs.
Now, add half the plant milk mixture, and toss again.
Add the remaining pasta water and plant milk mixture. Gently toss to coat.
Remove the pan from the heat.
Add the salt and pepper and lemon juice. Toss the pasta again. Taste and adjust seasoning for personal preference.
Sprinkle with parsley, thyme, and optional vegan parmesan cheese.