In a large bowl, combine by hand the squash, half of the onion, 1/8 cup egg substitute, 1/4 teaspoon salt, and 1/4 teaspoon pepper. In another large bowl, combine by hand the zucchini, half of the onion, 1/8 cup egg substitute, 1/4 teaspoon salt, and 1/4 teaspoon pepper.
Heat a large non-stick griddle over high heat; it will be hot enough when a drop of water sizzles when dropped on the surface. Squeeze out the excess liquid from both the squash and zucchini mixtures. Working in batches so as not to overcrowd the griddle, carefully drop 1 heaping tablespoon of both batters onto the hot griddle and flatten with a spatula to form pancake shape. Cook for a couple minutes on each side or until golden brown. Repeat until no batter remains. Keep warm in a low oven (250 degrees F) until all latkes are made, if desired.