Cook noodles to al dente according to package; drain and set aside.
Melt butter in a large skillet over medium. Add onions and 1/2 tsp salt. Cook, stirring, until deep golden, 20–25 minutes.
Sprinkle flour into onions; stir 1 minute. Slowly whisk in milk and broth until smooth. Simmer until thickened, 3–4 minutes.
Stir in tuna, peas, thyme, remaining 1/2 tsp salt, and cooked noodles. Mix well and transfer to a greased 9x9-inch dish.
Toss panko with olive oil and sprinkle and sprinkle cheddar over the casserole, then top with panko. Bake at 375°F for 15–18 minutes, until bubbly and golden.