To use different ports, I append a colon and the port# to the name or ip address in the setup: "mailserver.company.com:55". I have seen that you can also do this in the registry, but I haven't been able to get that method to work.
Secured connections are going to be a major pain with the built-in software. If you have control of your mail site systems, you could setup SSH or VPN, but it doesn't seem right to need to jump through those hoops. Look at
http://www.rainer-keuchel.de/wince/stunnel.html for CE SSL if you feel like exploring. There are other cool things on his site too.
The PocketInformant (.com) folks have an evolving app for mail that is a little more functional and they have security on their todo list. It currently relies on the built-in mail controls, so you don't get much more in terms of connectivity at this point.
-dcx