I pronounce it as N.E.S. and S.N.E.S. as well. When the Super Nintendo came out, I called the NES the "regular Nintendo" or the "original Nintendo". It also bothers me when I hear people pronounce them as words.
It seems like every video I've seen on YouTube has people pronouncing them as words, which is weird because almost everyone that's posted in this thread prefers to pronounce the letters.