Heat butter and oil in a large dutch oven over medium heat. Add pasta, shallots, and thyme and cook, stirring constantly, until most of pasta is toasted (it won't be evenly toasted), about 5 minutes.
Add wine, 1 3/4 cups water, and the pepper. Stir in clams and cook, covered, stirring occasionally, until clams open, about 10 minutes. Discard any clams that don't open. Remove thyme branch.
Meanwhile, put bacon in a medium frying pan and set over medium heat. Cook, stirring often, until bacon is crisp, about 8 minutes. Drain on paper towels.
Stir parsley and half of bacon into clams. Transfer to a large serving bowl and sprinkle with remaining bacon. Serve with lemon wedges.