Heat oven to 350°F.
Combine squash, zucchini, and salt in a medium bowl. Let the mixture rest for 10 minutes, then pour it into the center of a kitchen towel and wrap into a ball to squeeze out any excess moisture.
Melt butter in a medium skillet over medium-high heat. Add onion and cook for 5 minutes, or until soft and translucent. Add garlic and cook for 2 minutes, or until fragrant.
Add the squash-zucchini mixture and cook for 5 minutes, or until vegetables begin to brown. Reduce heat to low.
Whisk eggs and cream together in a large bowl and pour over vegetables in the skillet. Stir slowly, about 5 minutes. Eggs should resemble a soft scramble.
Gently fold in Gruyère, sage, red pepper flakes, and lemon zest, then pour the mixture into a 10-inch ceramic pie pan and bake for 12 to 15 minutes, or until the center is set. To test if frittata is fully cooked, gently press on custard about one inch from rim to center, checking for firm texture throughout.