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This is currently a known issue with Alteryx Server, and our development team is aware of the issue. The issue occurs when a Subscription has the "API Enabled" option set to YES during creation. The error does not occur if the subscription has the "API Enabled" option set to NO originally during creation, and is then changed to YES after the subscription has been created. The API Key and Secret will then appear as expected.
A workaround for now would be to create a new subscription and set the "API Enabled" option to NO during creation, and then change the value to YES afterward. You can then move the user into that subscription.
If you are currently in a situation where it is not feasible to create a new subscription due to the amount of workflows that exist in the subscription where you are having issues with the secret, please reach out to Support (email@example.com) directly.