I call BS.
Although I have an amazingly messy desk (well actually three desks, as well as a floor), I also know many excellent engineers that are incredibly fastidious, right down to keeping their pencils in an orderly arrangement.
The messy desk observation may be related to another well-known phenomenon, captured in the late urban critic Jane Jacobs’s famous dictum, “New ideas need old buildings.” I understand that FE Terman, when he was dean of the Stanford school of engineering, firmly resisted moving the engineering school out of its WWII-era quonset huts and into a new building, on the grounds that "no work gets done in new buildings." Investors who have funded a company's move into a beautiful new building just before the company spirals in might agree.
I have always had a messy desk! I am sure it is a reflection of my genius. That said, every so often (once a year..) I do clean it up (mostly rearrange the piles) and then can't find anything for weeks.. I think it is most efficient to keep things "where I left them".
Ha! Well, I have a couple stories along these lines: 20 some odd years ago I worked at what is now called the Lockheed Martin Skunk Works. There was a rumor that Sherm Mullin, who assumed the role of president for part of the time I was there, had seen a guy's very neat desk and had fired the guy on the spot! The idea being that if he had time to clean up his desk, he was not working hard enough! I took that as job security for me with my messy (not quite like Pease [RIP, RAP]).
Later, I worked at a small startup and had my own bench in the back of the lab, messy as all get-out. The technician was a real neat freak and commented one day how he couldn't understand how I could get any work done in such a mess (again not quite as bad as Jim Williams' bench, RIP). I said that it was very simple; I don't waste any time cleaning up!
I'm no genius, but my desk is sure messy. Not only that, my "stuff" also occupies the other two positions in my cube effectively giving me a "private" office. I think I would rather be the guy helping clean out Jim's place versus Bob's. We had a genius guy Fred G. (now retired) whose desk looked almost identical to Bob's. :-)