Is it correct that you use this plugin which creates the custom post type ‘WooCommerce Subscriptions’?
https://www.woothemes.com/products/woocommerce-subscriptions/

When a specific column, added by a Plugin, is not visible in the dropdownlist ‘Default columns’ in our plugin, this means that the plugin uses not the default way of adding new columns to the overview. Or they use some custom logic to show the columns on some specific pages. This can result in a case where we cannot access the columns on our setting page to remove or alter that column.

Unfortunately we cannot do anything about that in out plugin because this would require a very specific fix for this plugin. A workaround for your specific situation is to dive into the plugin and find the code that sets the column to the overview and see if there is any hook or filter you can hook into to disable the columns yourself. I cannot help you with this because I don’t have a copy of the WooCommerce Subscription plugin.