One a discussion is disabled, it no longer appears in the admin control panel to be re-enabled but it does show in the count of discussions.  How do you re-enable a discussion that was disabled?

Maybe by disable you mean delete???  There's a lock option which lets you lock threads so they can't be updated any more.  You can go back in and edit the last post to unlock it if you'd like.  If it's deleted I think it's deleted and you can't get it back.

I assume when you refer to "Discussion" you mean a "Forum" and not a "Thread", based on your description of Forum Manager. I tried in multiple installs to disable a forum, which worked like you said in terms of no longer showing up in the forum list in the site. However, I am still able to edit a disabled forum via the Forum Manager (I notice in Forum Manager that the checkbox is unchecked, like I should).