What about this? Basically it's a way to customize the text by adding a callback function to the functions.php file. I'm thinking, however, if you just return a space instead, then it should override it and not display anything.
// Replaces the excerpt "more" text by a link
function new_excerpt_more($more) {
global $post;
return ' ';
}
add_filter('excerpt_more', 'new_excerpt_more');
I got this from The Wordpress codex
Edit:
This is untested, but what if you do this:
// Replaces the excerpt "more" text by a link
function new_excerpt_more($more) {
global $post;
if ($post->post_type == 'your-cpt')
{
return " ";
}
}
add_filter('excerpt_more', 'new_excerpt_more');
To reiterate, I haven't tested this, but may get you on the right track (i.e. var_dump($post) to see how you can bend it to your will from within the new_excerpt_more function.