Hi,
No. The template.css file is not included in emails. In fact, none of the CSS of the website is included.
That's because the CSS that you can use in a email is different than what you can use on a website. So if you were to just use the standard CSS of the website, it wouldn't work properly.
That's why you can see the styles of the emails at the top of the HTML version (on versions previous HikaShop 3) or at the top of the email template if you edit it in an email (HikaShop 3.0.0 and higher) when you edit your emails via the menu System>Emails.
So I would recommend to directly edit the CSS there.
Here is a guide of what is possible in CSS in emails:
www.campaignmonitor.com/css/