If I have simple products with duplicate URL keys that are only visible and sold by way of a configurable product, is there any reason I cannot or should not just remove the url keys from all of the simple products under a configurable product? Other than I would need to recreate a url key if I wanted that product to be visible outside of the configurable product later?
In that case, it's better practice to use configurable product url as entry point, for example nike-shoes. On all simple products (lets say thay you have size & color variations), just append their parameters naturally, like nike-shoes-blue-40, nike-shoes-blue-42, nike-shoes-green-42...
There is no reason to use the same URL keys when Magento will append number at the end, which looks awful.