If you've read Woz's autobiography (iWoz) you know the guy is really nice and often times, it leads to him getting duped and misquoted by reporters looking to catch someone saying something flagrant and headline worthy.
I'd almost bet the case of Woz supporting patent trolling was yet another misquote.
Personally, I think it would be hard to deal with these kind of issues just as Iwata states. The issue you pointed out, where nintendo shut down a fan-made film based on the Legend of Zelda might have been necessary.
If the film were going to start actually turning a profit for the creator then they kind of crossed the line where they're profiting off someone else's intellectual property.
I wonder about this all the time. I log into Gmail with an encrypted connection (https). So if I send personal email from here, I'd hope that its off limits and they can't see it, but on the other hand... is it really?
If IT take a screen capture or grabs some key strokes from a personal email, I guess its technically not off limits.