Bring a pot of salted water to a boil. Boil the pasta shells for 7-8 minutes until al dente. Reserve 1/2 cup of the pasta water and drain.
While that boils, heat a skillet or wide pot on medium heat. Melt the butter in the pan, then add in the fresh thyme. Toss together for 1-2 minutes.
Lower the heat to simmer and add in the pumpkin puree, coconut milk, pumpkin pie spice and 1/2 tsp salt. Whisk together until smooth.
Add in the pasta water, starting with 1/3 cup, and nutritional yeast and mix well. Taste and adjust salt as needed. Simmer for 2-3 minutes on low.
Add the pasta into the sauce and stir together on low heat for another couple of minutes.
While that cooks, add the breadcrumbs to a small saucepan with 2 tsp of olive oil and pinch of salt. Toast on medium heat for 3-4 minutes to brown.
Transfer the pasta to a serving dish and top with the breadcrumbs right before serving. Garnish with a few leaves of thyme