Likely, unless the return is a PDF, you would have to come up with something to allow printing in a close format. (Note, even PDF is not perfect, it cannot be guaranteed to match what the author intended, since PDF software now allows the end used to adjust the file, such as line width, fonts, etc., and that does not even consider the fact that printer software is imperfect - such as really margin accuracy.) PDF is the one format you can count on to be close, assuming the end user does not muck up the settings.
Personally, I would not trust any built into PDF creation software password and/or encryption. PDF security is said to have been compromised, at least once recently IIRC. Since it is a common format, it is reasonable to believe there are hackers constantly looking to break the security. With that said, PDF security, with a kept up to date creation system, is likely good enough to say you took reasonable steps to be secure, if you are comfortable with that, and with your business insurance :).
For sending something securely via email, PGP type systems as Catherine mentioned, are likely reliable, provided the system in use handles the questions from the end user (unless you want to take on that support).
On the other hand, when I get "secure" messages from our charge card processor, it comes in the form of a message, with a link, for which I have to sign in to see the message. There is no support needed, as it is very clear what I have to do. It is a bit of a PITA, since the message eventually is shown to me as a tif file (an image), but I am completely comfortable their system is as secure as can be (since it contains data one would not want in the wild). While I do not use ATX, what G'maBee said about a client portal is very likely some sort of secure method to contact your clients, and possibly share data. Hopefully it is some sort of system like what our charge card processor uses, not just a way to send "secure" PDF files.