There are two different types of encryption: "encryption at rest" and "row level encryption".
What if someone gets access to your SQLite file? They have all your data. "Encryption at rest" protects you against this by encrypting the SQLite file itself. If someone steals your SQLite file it will be useless to them. sqlcipher provides encryption at rest. This is a good idea in general.
What if someone hacks into your application and injects SQL commands? What if they select
all your customer data? It doesn't matter if the file is encrypted, the SQL connection will decrypt it. To protect against this you can add a layer of "row level encryption". This is where your application encrypts the data it writes and decrypts the data it reads. The data being stored is encrypted. This is more complicated and has more performance impacts. Since the data is inserted encrypted, it is more difficult to search and index. Use it only for very valuable data that you're not likely to have to search. You're better off securing your application against SQL injection in general.