I've come up with the solution I want:
My problem was I've installed a local language pack which has generated several custom E-Mails. These E-Mails were stored in the database.
I simply had to change the used E-Mail in the specific setting in the backend.
For example in
System -> Customers -> Customer Configuration -> Create New Account Options I've changed the option Default Welcome Email to New account (Default Template from local).
This option (Default Template from local) will use the templates from the directory
magento/app/locale/.../template/email and not from the database.
As addition I've followed the guide and installed the plugin from https://www.yireo.com/tutorials/magento/magento-theming/1670-customizing-magento-email-templates
So I simply can copy the templates to my own theme.