Comment moderation on custom post types this answer shows moderation on custom posts. Is this possible with disqus?
Disqus pre-moderation rules are set on http://disqus.com/admin/settings/ and can't be administered via Wordpress. Currently there are only options to pre-moderate all comments, or comments from unverified users globally.
If you wanted this kind of granularity, you can always register a new Disqus shortname (which is a container for all of your comments/settings) and install the Universal code on those custom post types with your new shortname. Just remember to remove "default" Wordpress comments for those post types so you aren't loading it twice.
It's on that new shortname that you'd set a global pre-moderation rule and it'll apply to those custom post types.