Encrypted is certainly better than plain text.
Storing a password in the app, however, still has some issues in my mind. By doing so, you are essentially allowing anyone with control of your computer (the "hacker" in your question) to access your FTP server without credentials. At that point, they really don't need to decrypt your passwords at all... They can just log in and compromise the files on the server without ever knowing the password.
My recommendation is always to use a password manager that supports 2 factor authentication. Store your passwords there instead of within various apps written by various persons using varying levels of encryption.
Or use keys as @shadur pointed out in comments above... Protected with a pass phrase.