I agree, one of TweetDeck's persistent issues is that a person you follow could drop through the cracks and you'd never know you didn't have them assigned to a group. I don't have an "everyone" group, I just have 5 sub-groups (along with Direct Messages, Mentions, and Facebook). As it is now, I have to scroll to see them all, so adding an "everyone" group and hoping that I see the random tweet from any accounts not assigned to a group isn't really feasible.
I'd be happy if there was a way to search for unassigned accounts -- even just a search term like "unassigned".