Make filling: Using a spoon, scrape seeds from center of each zucchini half and slice crosswise into 1⁄4-inch-thick pieces.
In a large pot, combine zucchini, sweetener, butter, lemon juice, cinnamon, vanilla, and salt. Place over medium heat and cook, stirring occasionally, until zucchini releases juices and juices thicken, about 15 minutes. Remove from heat.
Make crisp: Preheat oven to 350°. In a medium bowl, whisk together almond flour, coconut flour, sweetener, and salt, breaking up any large pieces with fingers, if necessary. Add pecans and butter and stir until combined and clumps form.
Brush a 1-quart cast-iron pan or baking dish with butter. Scrape zucchini mixture into prepared baking dish. Scatter crumble over top. Bake until top is golden and juices are bubbling around edges, about 25 minutes. Let cool slightly before serving.