Preheat oven to 350°. Cook pasta according to package directions. Drain and rinse in cold water; drain again.
Meanwhile, in a large skillet, cook beef and onion over medium-high heat until beef is no longer pink, 6-8 minutes, breaking beef into crumbles; drain. Stir in tomato sauce, ketchup, mustard and pepper until blended. Stir in 3/4 cup shredded cheese.
Spoon about 2 tablespoons filling into each shell. Place in a greased 11×7-in. baking dish.
Bake, covered, until heated through, 12-15 minutes. Sprinkle with remaining cheese; bake, uncovered, until cheese is melted, about 5 minutes. If desired, serve with optional toppings.
Freeze option: Cool unbaked casserole; cover and freeze. To use, partially thaw in refrigerator overnight. Remove from refrigerator 30 minutes before baking. Preheat oven to 350°. Cover casserole with foil; bake as directed, increasing time as necessary to heat through and for a thermometer inserted in center to read 165°. If desired, serve with optional toppings.