I went to a Pizza Hut near Rockefeller Center in Manhattan at some point in the mid-90's. I just remember the prices there were about 3 times what we paid on Long Island. Actually, from Suffolk County as you drove closer to Manhattan, prices would creep up on everything, most noticeably on fast food.
I was at a Denny's in San Fransisco a couple of years ago, and I remember the entrees cost about $12-$20.
So yes, I imagine that at a handful of fastfood outlets in the central business and tourist districts of the biggest cities, it's just not economically feasible for them to do the $.99 menus.