It's not just UFC. Meltzer has covered PRIDE, K-1, Pancrase, etc. for years and those promotions have cropped up in his awards periodically.
I believe Meltzer started covering mixed martial arts due to the blending of MMA and worked wrestling matches in Japan in the 1980s which stemmed from the foundation of the UWF (Japan) in 1984. By the early-1990s, there were a number of Japanese wrestlers competing in MMA promotions, all of which were covered by the Wrestling Observer.
Meltzer has covered UFC since the inaugural event in 1993 and his readers seem perfectly happy with the fact as a lot of wrestling fans watch MMA as well.
P.S. I agree about boxing being fake. I watched the Lewis/Holyfield fights and Amir Khan's pro debut, and they were blatantly fixed.