Preheat the oven to 400°F (200°C).
Crumble the fresh chorizo into a skillet. Add the onion and garlic. Cook over medium heat until the chorizo is browned, about 10-15 minutes, stirring occasionally.
While the chorizo cooks, wash your zucchini and chop off the stem end. Cut them in half lengthwise. Use a melon baller to scoop out the middles, forming the boats, as shown. Arrange the boats in a single layer in a large tray pan. Save the zucchini middles to use in other recipes.
Add the strained tomatoes to the chorizo mixture. Allow it to simmer down for 10 minutes, stirring occasionally. The results should not be very liquidy.
Evenly fill your zucchini boats with the chorizo mixture using a spoon.
Top the filled boats with the pepper jack cheese shreds.
Cover the pan with foil and bake in the heated oven for 35 minutes.
After baking, garnish with the cilantro. This makes 4 servings of 3 zucchini boats (i.e., 3 zucchini halves) each. You may end up with more or fewer boats per person depending on the size of the squash you start with!