Shared Taxonomy

Is it possible to have a shared taxonomy with 2 custom post types that can be filtered.

I want to display the category title and then list below all the posts within that custom post type related to the category. The problem I am encountering is if the shared category is only used in the other custom post type the category title will display even though it technically has no posts to display under it.

I only want to display categories and posts for that custom post type. If the category is not being used in that custom post type it should not display the category title since it has now posts.

Thanks!