Will the mail and the website be hosted on the same server?
If so a SSL connection to the users POP3 box is about as good as it can for this application.
I would suggest securely processing the orders online rather than sending the information via email for offline processing though.
There are alot more liabilities in handling orders that way versus processing it entirely online or at least keeping the users information in a secure location online to be reviewed manually. Imagine if a virus threat or spyware application farmed the users email box and forwarded out a customers identity/payment information?
In addition, there are new rules coming up from Visa/Mastercard regarding the storage of customer payment information. My suggestion has always been that unless you have a recurring need to bill someone, delete their payment information promptly from your database.
If you need a decent cart system, that has served me well, we have been mostly happy with the product from
They are slow to respond to custom development request even after you pay them a deposit though - watch that part.. The product itself is fairly sound though and reasonably priced. There are other solutions out there to such as OScommerce
- its open source! You can't beat the price

. Used with the right payment processing gateway and a policy to remove customers payment information (not sure if you can automated that or not) after a predefined time & properly setup hosting account it can do a great job as well.
I don't claim to be an ecommerce expert, but.. I hope that helps.
Thanks.