If you mean in red, blue, and yellow they didn't mean to. Back then they didn't have such wonderful music. You can notice this in old games such as Super Mario Bros, Starfox and others. If you mean in Gold and Siver the music was changed probally because better sound qulatiy and a spooky rumur that's a bit extreme for young children.
FYI: If you want know about the rumur type in at youtube lavender town myths.