I just tried out 7zip for encrypting. The only problem is that the encryption feature is obscure and require some automation.
What do you mean? It's shown right in the archiving window:
The command-line version supports it as well, of course.
One warning: the default encryption method for zip files is ZipCrypto, which is totally insecure. Either use the 7z format or use the AES-256 encryption method for zip (which makes these files incompatible with most zip programs).