Heat olive oil in a skillet over medium heat and cook zucchini and squash until tender, 5 to 10 minutes. Season with salt and pepper.
Melt butter in a separate skillet over medium heat. Add shrimp and garlic; cook until shrimp are bright pink on the outside and the meat is opaque, about 2 minutes per side. Add green onions and seafood seasoning and stir to combine. Remove from heat.
Scoop half of zucchini-squash mixture into a 9x13-inch baking dish using a slotted spoon. Add shrimp and skillet drippings. Sprinkle 1/2 cup Cheddar cheese, 1/2 cup mozzarella cheese, and 1/2 cup habanero pepper cheese on top. Add the remaining zucchini and squash mixture and top with remaining cheeses.
Bake in the preheated oven until gooey and bubbly, about 30 minutes.
