Heat a large stockpot over high heat. Add onion, garlic cloves, thyme, and oil. Cook for 15 to 20 seconds; add clams and wine, cover, and cook until most of clams have opened. Set aside until cool enough to handle. Strain and reserve wine broth.
Pull meat out of clam shells; roughly chop, and set aside. Separate shells, and rinse well.
In a large sauté pan, melt butter over medium-high heat. Add salami, and cook for about 2 minutes. Add shallot, chopped garlic, and red pepper, and cook until garlic and shallot are soft. Add 1½ cups reserved wine broth, and bring to a boil. Remove from heat, and stir in clams, parsley, and lemon zest and juice. Fold in cheese and bread crumbs until very well combined. Taste, and adjust lemon, salt, or red pepper to taste.
Divide mixture among clam shells, creating small mounds. Press and shape mounds firmly with your fingers. Place in an even layer on a large rimmed baking sheet.
Bake until heated through and tops start to get a little crispy, about 8 minutes. Serve with a generous squeeze of lemon.
Recipe by Louisiana Cookin' at https://louisianacookin.com/baked-stuffed-clams/