Place wire rack on a baking sheet and arrange squash slices in a singe layer. Sprinkle with 1 tsp. salt. Let stand 30 minutes. Rinse well under cold water then pat dry with paper towels. Place squash and onion in a glass bowl.
Combine water, vinegar, maple syrup, and red pepper flakes with remaining 1 tsp. salt in a small saucepan. Bring to a boil and pour over squash. Weigh down squash with a plate, then cover and refrigerate at least 2 hours or overnight.