As far as a T versus E10 rating goes... it's true that previous versions sold just fine, but Nintendo is probably (this is speculation on my part) looking at Smash for Wii U as a system-saver. They need it to move as many units as absolutely possible. That means wanting the widest audience possible. If the ESRB told them "Tharja goes, or you get a T rating," then the smart business move is to drop the trophy of a non-playable girl in a metal bikini. I don't like it either, but I fully understand why this might have happened. Smash 4 has been in development for years, is going to be a major profit source on the 3DS, and is their best chance to really push the Wii U to be a successful system. Ensuring this is seen as a E10 title rather than a T one goes a long way.
When it comes to emailing Nintendo about this... that depends on when you do it and what you hope to accomplish. They're probably not going to reinstate the trophy. If you email them about it before October 3rd (US release date), Nintendo's western branches are going to be required to just be all "We have no idea what you're talking about" in response. Also, your email will go to a general customer service rep. They won't be able to directly change the situation. If Nintendo gets enough emails about it, they may have food for thought on later games. Still, all you'll directly get for emailing them is a quick and generalized reply from someone far removed from Smash development. If you're okay with just creating a very tiny blip on Nintendo's radar (a lot of tiny blips eventually become a big one, after all)... then go for it.
It also depends on what your 'demands' as a customer are. If you're threatening a boycott over the Tharja trophy (and I'm not saying you are, but you didn't explain your exact motives so I have to explore the idea)... that may be going a bit far; there are reasonable explanations for what they did, ones probably brought on by the ESRB, business circumstances, and society today. If you're just hoping they'll be more bold about this sort of thing in the future, that's cool. Let Nintendo know you have their back even if a game gets a T rating, that you'll still support it with your money.