man zip
Da página do manual:
-e
--encrypt
Encrypt the contents of the zip archive using a password which is entered on the terminal in response to a
prompt (this will not be echoed; if standard error is not a tty, zip will exit with an error). The password
prompt is repeated to save the user from typing errors.
Outra opção é a criptografia SSL, por exemplo:
openssl des3 -salt -pass pass:password -in file.txt -out encfile.txt
Talvez você possa TAR a pasta antes de usar o openssl para criptografá-lo.
man openssl