Coatings don't fade. If your lens is clear and clean it is performing as good as it can. Look thru it at a light bulb, and move the lens around and see if you see any internal haze? If so, this can reduce contrast, and can be professionally cleaned. The 645 lens line is newer and may be designed with more contrast in mind. It is not a coating thing, in my opinion. Adding a multi-coated filter to any lens will not "improve" the lens. A polarizing filter can be used at times to add contrast, by darkening skies, and eliminating reflections on things. I have had and use an RB-67 for almost 30 years now, with the 90, as well as the 50 and 180. I have never felt a lack of contrast in my work with this camera system.
All lenses can be recoated, but normally it is only the front surface of the front element that gets worn, so the cost is moderate...but if you are considering recoating every element in the lens, you are better off just purchasing another good used lens. The lowest cost coating service is Arax in the Ukraine, and he charges about $30 per element, and if your 90 has the average 5 or 6 elements then the cost will be about $200 including shipping. You will have to take the lens apart and just send him the glass elements. he does no disassembly. So you see, you could probably buy another 90mm lens for the same or possibly less.