This sauce can be made with or without tomatoes. If you're using tomatoes in the sauce, score the skins on the bottom of the tomatoes with a large X, being careful not to cut deeper than the skin. Bring a small pot of water to a rolling boil, add the tomatoes and cook 1 minute then remove with slotted spoon or tongs, cool a minute or 2 until you can handle, then peel the skin and dice the tomato into small pieces.
Place the clams, wine and clam juice in large pot and bring to a boil, cover, reduce heat to a simmer and cook 8 to 10 minutes to open the clam shells. Scoop out the clams and shuck them, place in food storage container and cool completely. Store the clams in the refrigerator until ready for use. Strain the stock and reserve, wipe out the pot and return to the heat.
Meanwhile, make a seafood paste by adding the red onion, chile pepper, lemon zest, garlic, thyme, parsley, and bay leaves to the food processor and pulse-chop into a thick, but finely chopped, speckled paste.
Heat about 1/4 cup olive oil, 4 turns of the pan, in the clam pot over medium to medium-high heat. Add the anchovy filets and melt them into the oil, 1 minute or so, then add the paste and stir 2 minutes. Add the reserved stock and stir to combine. Add the tomatoes, simmer 5 minutes, then cool the sauce completely and store for make-ahead meal.
To serve, bring a large pot of water to boil for pasta. Salt water and cook pasta to al dente.
Meanwhile, heat the sauce over medium heat. Once the pasta has been dropped to cook, stir the clams into the sauce and simmer a few minutes. Add a ladle of starchy cooking water to the sauce and toss with pasta 1 to 2 minutes for the flavors to combine and absorb into the pasta.