Cook the pasta according to package directions. Reserve 1 cup of the salted, starchy pasta water before draining.
Place a large skillet over medium heat. Pour in the olive oil and swirl it around. Add the shallots and stir. Keep sautéing and stirring the shallots until they are very soft, about 4 minutes. Add the thyme and cook for an additional minute, being careful to not allow the shallots to brown on the edges.
Add the corn kernels to the skillet and stir. Season the corn liberally with salt and pepper. Keep sautéing and stirring until the corn is tender and bright yellow, about 8 minutes.
Transfer half of the sautéed corn mixture to an upright blender. Pour in ½ cup of pasta cooking water, non-dairy creamer, nutritional yeast, lemon zest, and lemon juice. Blend this mixture on high until completely smooth and creamy.
Pour the pureed creamy corn mixture back into the skillet with the remaining corn. Add the drained pasta to the skillet as well, along with some more salt and pepper. Stir to evenly coat the pasta. Bring the pasta up to a strong simmer, adding more of the pasta cooking water if it seems to be drying out a bit. Taste the pasta to check for seasoning and add more salt, pepper, or lemon juice to your liking.
Serve the pasta hot with vegan “parmesan,” ground black pepper, and chili flakes.