How to Make It
Melt butter in a small saucepan over low, stirring occasionally. Stir in bonito flakes. Remove from heat, and let stand 10 minutes.
Pour butter through a fine wire-mesh strainer set over a medium bowl. Press bonito flakes with a rubber spatula to extract all the butter. Discard bonito flakes. Pour infused butter into an airtight container, and refrigerate until ready to use.
Cook spaghetti according to package directions. Drain pasta, reserving ½ cup cooking water.
Heat oil in a large skillet over medium. Add shallot, garlic, crushed red pepper, and thyme; cook until shallot and garlic are softened, about 2 minutes. Add clams and white wine; increase heat to high. Bring to a boil; cover and cook, shaking occasionally, until clams open, 4 to 5 minutes. Transfer clams and liquid to a bowl; set aside. Discard thyme and any clams that do not open.
Return skillet to medium-high. Add reserved cooking water and lemon juice; cook until slightly thickened, about 2 minutes. Remove from heat; whisk in bonito butter and salt. Add clam mixture and pasta; cook over medium-low until heated through, about 2 minutes. Divide among 4 bowls, and top with chopped herbs. Serve immediately.