Prestige of publishing in special vs regular journal issue
I have not been a journal editor.  But I have dealt with many journal editors, and in my experience the kind of thing they are most concerned about is maintaining and elevating their journal's standards at all times.  So I have to imagine that when they put together a special issue, they take pains to ensure that this does not result in any measurable lowering of their journal's standards.

In my branch of mathematics, special issues are not that common but not unheard of either.  I have never noticed any difference in the quality of the papers published in these special issues.  Also in my experience people may not even list on their CV that the publication has appeared in a "special issue".  

I have on the other hand been on many hiring committees, and I have not heard a thing about this.  Again though in my field this sort of publication is relatively uncommon and it may even escape our notice.  I suppose that if a candidate had ten publications and they were all in "special issues" that might be curious.  

All in all, in my neck of the woods there is nothing to worry about here.