I've heard it countless times; my sister who played the games has heard it too. Yeah, the tune is a little creepy, but that's about it. It's my opinion that a lot of these types of "conspiracy theories" are more of the satirical type.
You've played the ORIGINAL Red and Green? As in, the ones in Japan only, that were edited before they came to America? They didn't have any color, a few sprites were different, and some music was changed. It's not the same game as Blue and Red.