If you do this in the background (in your case with Hazel), then, of course, the file(s) will be unencrypted.
There is no user interaction where you are being asked if you want to encrypt.
The only way here to get encrypted files is to point Hazel to save the file(s) to an encrypted folder. Then, the file(s) will be automatically. But I think, is not so convenient for you, you are saving to different folders, am I right?