I never thought Nintendo sued people due to their bottom line being hurt. I always thought they did it strictly for the principle.
I mean, is the github pirate emulation audience the same people who pay full price for Princess Peach day 1 if they can't emulate it?
Nintendo believes in the simple concept of, "If you don't use it you lose it." They believe if they see copyright infringement and don't act on it, they may not be able to act on it in the future. If they permit someone to use the characters without permissions by simply not acting, then the next person who did it and got sued would used the previous incident against them in court.
If you owned a logo, say the one for neogaf, and then allowed everyone to use it all the time, then decided to sue this one guy who was using it in a way you didn't like, what would that guys defense be in court?