Cut a lengthwise 2cm thick slice from each zucchini. With a spoon, scoop out the flesh, leaving a shell intact all around the zucchini. Discard or save the flesh for another use. Chop up the long slices of zucchini.
Heat the olive oil in a frypan over medium heat and cook the chicken sausage, breaking the meat up as it cooks, until the sausage has begun to brown, about 8 minutes. Sprinkle in the chilli flakes and season with salt and black pepper. Stir in the chopped zucchini, onion and garlic and cook until the onion is translucent, about 5 minutes. Scrape the sausage mixture into a bowl and stir in the tomatoes, bread crumbs, Parmesan cheese and basil until the stuffing is thoroughly combined.
Lightly stuff the zucchini boats with the stuffing, place the zucchini into a baking dish and bake until thoroughly heated through and beginning to brown on top, about 30 minutes.