As it sounds, special issues of journals focus only on a very specific sub-field of the scope of the journal. Usually, special issues are handled by the guest editors and they invite researchers of that specific field to submit articles (solicited articles) for the special issue. However, there could be exceptions. In my view, there won't be additional prestige or reputation in publishing in the special issues than publishing in the regular issues. However, quick responses, relatively quick online publishing of accpted articles, possibility of reaching to a specifc readership may be considered as some of the benefits of publishing in them.
In addition to publishing selected papers in conferences, a publisher can announce a special issue journal to concentrate on a particular set of fields which may be a subset of its overall scope.
One main point to note is that special issues have an additional advantage that they are time-bound. That is the dates for first review result, acceptance/rejection, and publication, are all scheduled. Although sometimes, the dates may be subjected to change, this is in contrast to regular journals where the time-frame may not always be estimated.