Whisk water, ketchup, soy sauce, cornstarch, honey, sesame oil, and red pepper flakes in a bowl. Stir shrimp into sauce mixture until coated.
Heat a wok or a large skillet over medium-high heat and add vegetable oil; cook and stir garlic and ginger in hot oil until fragrant and garlic begins to soften, 1 minute. Discard garlic and ginger, leaving oil in wok. Cook and stir broccoli, red bell pepper, onion, yellow squash, zucchini, and mushrooms in oil until slightly softened, about 5 minutes.
Stir shrimp and sauce mixture into vegetables; cook and stir until shrimp are hot and sauce has thickened and coated shrimp and vegetables, 3 to 5 more minutes. Serve over hot cooked rice.
