I have never understood that statement. Kubrick didn't own any of the props or costumes, MGM UK did, so he couldn't order the destruction of the studio's property. What I have read, is that the production of 2001 ran so long and took up the entire resources of the studio, so that it couldn't rent it's self out to other productions. The loss of revenue collapsed the studio, and all of the props and costumes were put into outside storage. Eventually MGM got tired of paying the storage costs and had everything trashed. Not just the 2001 properties, but everything from all of the studio's productions from it's beginnings. A lot of film history was lost.
Some items did escape, the Discovery space maneuvering packs were used as set decorations in a couple of BBC sf shows. A Moonbus seat was used a the sub drivers seat in the SkyDiver set of UFO. The models were given away because of their size, and MGM didn't want to pay for their storage. They were large, and somewhat fragile, so storage would be a problem.
As for the destruction of 2001 props, it's tough to tell what really happened there. I remember reading a while back that somebody found the giant studio scale Station 5 centrifuge in a field somewhere in England. Apparently not destroyed like originally thought, but if I remember correctly it was trashed and vandalized over the many years it was sitting out there. Such a shame..
I always thought his stuff was always destroyed as well, every movie he did cause I was trying to find stuff from a clockwork orange, but was told it was all destroyed. Also wouldn't mind having that police uniform from the fifth element.
In that display the Discovery Command Module is almost certainly from "2010 the year we make contact". I would wager that the other spaceships in that case are replicas. Possibly the Discovery coveralls costume is authentic, there is one of those floating around.
Regarding the Sci-Fi Archive, I met Arnaud and some of his friends when they were here in Los Angeles last month. Nice guys. The large Discovery Command Sphere is indeed the original filming miniature for "2010". I restored it with the help of Carson Dyle prior to its sale.