Preheat oven to 350°F. Line a baking sheet with parchment paper. Peel and slice the squash into 1/2-inch slices. Roast for 25–30 minutes, until fork tender.
Mash or blend the roasted squash until smooth. Stir in olive oil, nutritional yeast, nutmeg, and salt until evenly combined.
Create a mound of flour on a cutting board and make a well in the center. Add the squash puree and knead gently into a dough. Add more flour if too sticky. Let rest for 15 minutes.
Cut dough into four portions. Roll each into 1/2-inch ropes, then cut into 1/2-inch pieces. Boil in salted water until the gnocchi rise to the surface (3–5 minutes). Drain and set aside.
In a large skillet, melt olive oil and butter. Add walnuts and toast 3–5 minutes until fragrant. Remove and set aside.
Add cooked gnocchi to the pan and brown for 2–3 minutes. Push to one side and add shallot, sage, pepper, and salt. Sauté 3 minutes until fragrant.
Add white wine (or pasta water), scraping up brown bits. Simmer 5–7 minutes until reduced and gnocchi are crispy again. Return walnuts to pan and toss to coat.
Serve warm, topped with more black pepper or fresh herbs. Store leftovers in the refrigerator for up to 5 days.