Definitely a nice to have, i would think if logged in as admin it would still show the categories though, but just say [hidden] next to them, so you can get to them and see them when designing the site and populating it. If you truly wnat to hide in all regards the 'hidden' flag on the category editor is the proper route, this will really hide the category across all of the store.
Now some people put considerable effort into SEO of their category pages and then poof they disappear, we want to consider this...I'm thinking it would still be active in all sitemaps and link lists, just not the active left navs/top nav controls or subcategory lists. That way they are still there, you can still browse to them, just not quite as easy. But engines still want to see them linked from the home or some other proper page though for good pagerank. Am I making too much of this part of the issue?
Attributes already do just this. Also, attributes can even be tied to inventory to hide when no "inventory" exists. Just a footnote.
Ed Sturrock
AmeriCommerce Product Manager