You have an option in the view menu to not show unversioned files but this is ignored by your commit dialog. There is an option  suggest to "add untracked files" for the commit command, but not to hide them.

I will not comment anymore !. Other than this I am impressed by SmartGit so far.

I am porting legacy software and the unversioned files will typically be tracked at a later date but I am not ready yet. I currently use TortoiseHg and this works the way I described.