Bring a large pot of water to a boil. Once boiling, add the pasta and a heavy pinch of salt and cook until al dente, according to package instructions.
Meanwhile, heat a large skillet over medium heat. Add the pancetta and cook, tossing occasionally, until the fat begins to render and it becomes slightly crispy, about 4 minutes.
Add the garlic, shallots, and red pepper flakes and cook, stirring, being careful not to burn, about 2 minutes.
Add the heavy cream, lemon zest, and black pepper and stir to combine.
When the pasta is done cooking, reserve about 1/2 cup pasta water. Drain the pasta and add to the skillet and toss in the sauce. Add the Pecorino Romano, lemon juice, and a pinch of kosher salt.
Add about 1/4 cup of the reserved pasta water and toss until the cheese melts and the linguine is glossy and well coated. If your sauce seems too thick and the pasta isn’t glossy, add the remaining 1/4 cup of pasta water and continue to toss until well coated. Remove from the heat, taste, and add more salt, to taste.
Serve with a sprinkle of Pecorino Romano and a pinch of crushed red pepper flakes, if desired.