UPDATE
I’ve merged some of the most important branding and styling features for wp e-commerce into one bundle called “wp e-commerce shop styling”
Find more information here
As far as I know HTML mails are already supported by nearly every mail client.
I’ve heard of a few nerds out there, reading there mails still in plain text (maybe even in command line?), but the majority of your shop customers prefer formatted mails.
Mails sent from your WP E-Commerce store look a bit old fashioned.
In my opinion the mails of your store are an additional chance for advertising and showing your brand.
There’s a nice wordpress plugin to style your mails according to your corporate identity:
wp-e-commerce-style-email by Jacob Schwartz offers you an additional theme file to wrap your mail content.
To keep the formatting of the plain text mails it replaces all newlines with html newlines.
It doesn’t make perfectly beautiful mails and it needs some coding to generate the template file, but it does its work very well and your mails look much better than before.