It's worth seeking out guanciale, an imported, spice-cured Italian bacon, to add depth of flavor to the linguine and clams. But if you cannot find it, pancetta is a good substitute.
Cook guanciale in a large pot over medium heat until crisp, about 15 minutes. Transfer to a plate using a slotted spoon. Heat oil in pot. Cook garlic, red-pepper flakes, and fennel seeds until golden and fragrant, about 2 minutes. Add vermouth. Bring to a simmer. Add squid. Cook until just cooked through, about 1 minute. Transfer to plate with guanciale using slotted spoon.
Add cockles to pot. Cook, covered, until opened, 5 to 6 minutes; discard any unopened ones.
Meanwhile, bring a large pot of salted water to a boil. Cook linguine until al dente. Drain, reserving 1/2 cup cooking liquid. Mix guanciale, squid, pasta, and reserved cooking liquid into cockles. Drizzle with oil.