The releasing the file system/database layout would not be much of security issue (security that is worth more than $0.02 works when you how it is done).
Just check out any crypto forum and you will that the security model that they use assumes that the attacker already knows how the system is constructed and which algorithms are in use. The reason is pretty simple, if your security is dependent on keeping the layout secret, than anybody that finds the layout can then break your security. Like the OP said, the people working on the system know the layout (and they don't have jobs for life). Any copies will expose the secret for everyone. In the crypto world, security is based on the idea that without the secret key, every copy must must be broken using methods that are little faster than brute force.