Bring a large pot of water and 2 teaspoons salt to a boil over high heat.
Add the pasta and cook until al dente, 8 to 9 minutes.
While the pasta is cooking, in a large pot over medium heat, melt the butter. Add the garlic and cook, stirring, until fragrant, 30 to 60 seconds.
Add the zucchini and 1/4 teaspoon salt to the zucchini and sauté, stirring frequently, until softened, 2 to 3 minutes. Season with black pepper.
Switch to a whisk and sprinkle in the flour. Cook, still whisking constantly, for 1 minute.
Still whisking, gradually add the milk and increase the heat to high. Continue to whisk until the milk comes to a brisk simmer, reduce the heat to medium-low, and maintain a simmer until the sauce thickens, 5 to 7 minutes.
Add the mustard, nutmeg, smoked paprika, and cayenne pepper and whisk to combine.
Gradually add the Cheddar, fontina, and Gouda cheeses in handfuls, stirring well after each addition, and cook until the cheese has completely melted, 3 to 5 minutes. Season with 1/2 teaspoon salt and black pepper.
Drain the pasta. Add the pasta to the cheese sauce and stir to coat the pasta thoroughly. Mix in half the bread crumbs and stir to combine.
Sprinkle with the remaining bread crumbs and serve immediately.