Trim both ends off courgette; cut in half lengthwise. Cut a thin slice off the backs so each half sits flat. Scoop out the pulp, leaving a 1/4-inch shell. Finely chop the pulp; set aside.
Place the courgette halves in the oven. Sprinkle with 1/4 teaspoon each salt and pepper. Cover with foil and bake it until tender-crisp, 10 minutes. Whisk oil, vinegar, shallot and the remaining 1/4 teaspoon each salt and pepper in a medium bowl. Add tomatoes, cheese, basil and the reserved courgette pulp; toss to combine. Divide the filling among the courgette-canoes.