Bring large pot of water to boil.
Meanwhile, warm oil in large cast iron skillet or large frying pan over medium heat. Add shallots and cook, stirring often, until translucent, approximately 4 minutes. Add garlic and thyme and cook for 1 more minute. Add corn kernels to skillet and season with salt. Increase heat to medium high and sauté corn mixture until corn is bright yellow and tender, approximately 4 minutes.
Transfer warm corn mixture to blender; add nondairy milk, nutritional yeast, lemon zest, and lemon juice. Blend until smooth and creamy.
In boiling water, cook pasta as directed on package; reserve 1 cup of water before draining.
Pour blended corn sauce back into skillet; add drained pasta and 1/2 cup reserved water. Set skillet over medium heat and stir until well combined and warmed through. If sauce gets too thick, stir in additional reserved pasta water. Season with salt and lemon juice, to taste.
To serve, divide pasta among 4 serving bowls and garnish with freshly ground black pepper and additional thyme leaves, if desired.