We want to style the activation mail that our user get when they register. Can we do that?
Yes, you can do everything 
The activation e-mail is here (body.html and body.txt). Instead of directly modifying the template, a better way to separate your customizations is to create a theme. This takes a while but it lets you customize and override any template or parts of templates. A simple introduction. It’s easier to change some CSS or images first for practice, and when it works start changing the templates.
Of course, directly modifying the file (without a theme) also works, but this makes upgrading Open edX harder because the new code can conflict with your changes.
Thank you very much
We use a theme, but we don’t use edx ace and our activation email text is inside a file called activation_mail.txt
do we need to install ACE or to do something else before we create there directories and files in the theme?
I think you find activation_mail.txt which is a different e-mail (the text is different from the other e-mail I linked). I’m not sure which one is used, but you can find the one which is used. Then to replace it, you create files in the theme, with the same path of the files that you want to overwrite.