I'm tempted to say no (outside of historic/preservation usage, of course)
1st, the AAR designination of Well-Hole flat cars is interesting in and of itself:
"FW" -- Flat well-hole car for special transportation of plate-glass, etc. This car is a flat car with hole in middle to enable lading to be dropped down on account of clearance limits (1/17-4/99).
Plate glass? I can't image that going in any thing but containers (or maybe boxcars) if by rail - well, maybe in special packages on regular flats, but no need for well-hole.
Otherwise, a lot of times transformer transport is mentioned, but that could go as easily via depressed center flatcars, and there's a decent number of those in revenue service nowadays, so again no need for well-holes - actually, I was wondering what advantage did well-holes offer vs depressed center - was it soley a construction/structural strength issue, when I found this cool tidbit (and it does involve glass):
March 25, 1936 The 200-inch mirror blank for the Palomar observatory begins its cross- country trip aboard a well-hole flat car [NYC 499010]. At the time it was shipped it was the single most valuable item ever shipped by rail. Railroad Vice-Presidents accompanied the special train to make sure there were no problems. As it traveled in the well-hole flatcar, the mirror was only inches above the rails.
(from
this website) - I wonder if the sides were used to protect this kind of load (the mirror had to be secured anyway so it wouldn't shift around in transit, was having sides a plus in this instance?)