SQLCipher does not distinguish between “unencrypted database” and “encrypted database with the wrong passphrase”. Ideally, you would track whether or not the database is encrypted. And, at the time you decide that you want to encrypt an unencrypted database, you will need code to encrypt it. This Java method will encrypt an existing unencrypted database.
The getDatabaseState() method on that utility class will attempt to determine if a database is encrypted or not, by trying to open the database with an empty passphrase.