Many probably die from predator strikes and are taken away to be eaten. And like a lot of animals, injured or sick squirrels hide, hoping to heal or recover, and when they die, the bodies aren't in plain sight. I suspect in a city, the biggest mortality factor would be traffic. Crows or vultures will eat the carcasses. Ants, insects, microorganisms...all of them work to utilize a dead animal so the bodies don't lie around for long.
Nature doesn't let a lot go to waste.