Magento 1 On storeScope flatrate shipping method is disabled but when accessing site in checkout it is still possible to choose it to complete order. What could be the problem? There are no hardcodes in code for this.
System Config is broken into 3 scopes: default, website and store.
Settings at the "default" level will be overridden by the "website" level, and "website" level configs will be overridden by the "store" level.
Store is typically only designed to deal with language changes, such as converting the Flat Rate Shipping title from english to another language. Magento often does not even display enabled/disabled actions at the store view level.
Most likely you want to switch to the website level, and check the setting there.