Let's be calm about this: The letter does not tally with what the OP is suggesting. I'm more concerned about minimum price agreements (requirements) that stores must play with, regardless of whether it makes good business sense.
It makes perfect sense that Nikon would not want non-certified repair centers, who probably did not have access to all the Nikon literature and support, fooling around with their cameras. Of course, I do not know what goes around with a certification, and there may be a valid question about it if it costs a fee. However, as a car owner, I expect my car service to include professionals who have been judged competent to do the work. I believe that as it is a large and regulated industry, there are non-corporate sources of certification for individuals and shops can do auto work, but you still need access to the materials. For cameras, there isn't as much demand to have university programs to certify technicians, as compared with autos (or computing certifications, i.e. the CompTIA A+ - the Microsoft MVP is not an exact example because it is more or less an award for outstanding achievement in a field, and not the result of an exam), and there isn't quite as much of a public interest argument in making sure that certification is an open and vendor-neutral process (though you might agree).
It's a bit like my saying that if you sell my bent plastic and tungsten shims that you should be 'certified' in their use and installation to sell them. It may seem nonsensical, but if the market is not as essential to public welfare as auto or computer certs, then I may well expect more freedom as universities won't be jumping to certify, and there's not much of an argument that I need to be regulated in terms of allowing others to certify users of my specialist product.
The argument is rather whether I am acting as a monopoly and restricting the availability of certs, which the Nikon letter does not inherently suggest. If their actual business practice is to use this as another tool to enforce price controls, or to make loads of cash off a needlessly expensive cert process, then there is a case, but simply requiring a cert doesn't seem to be a problem to me.