Ok, I found the issue here: the obfuscate filter needs to be added to the output from eme, but even then the filter wouldn’t work since I already obfuscate the email (using ascii encoding).
Anyway, in trunk I added a filter for email encoding, so if you define the filter like this in your theme functions.php file:
add_filter( 'eme_email_filter', 'c2c_obfuscate_email' );
it will be obfuscated in the way of your choice (in this case the filter function comes from the “Obfuscate E-mail” plugin)
In the same way, you need to add the filter functions of your choice to “eme_general” and “eme_notes” for your quotation marks.