They likely having taken action as Project M hasn't actually harmed the sales of Super Smash Bros at all, if anything, it improved the sales of Super Smash Bros. Brawl, since the disc is required to run the game and the PM Team directly stated they will not create a version that works without it. Since they'd tried to stay on Nintendo's good side as best as possible, they haven't run afoul of them.
The problem though is that Nintendo can not officially recognize nor condone Project M as then we get into the sticky Copyright Law issues. From what I've learned from my connections at Capcom, while Fan Works can be Amazing and they may even love them, if they are seen acknowledging them then Copyright Lawyers could claim they aren't actively 'protecting' their IPs as they are letting a 3rd Party use their copyrights without direct legal permission. If they then do not come down on said project with a Cease & Desist Order, then they risk losing their IPs to the Public Domain. I can't pretend to understand why that is, but it is how it works.
So, in essence, by Nintendo fervently deleting any mention on MiiVerse of Project M and refusing to even acknowledge its existance, they are actually Protecting the team, in a way, as if it was brought up in court that Project M was mentioned and allowed to be discussed on Nintendo's official social network and that Nintendo had knowledge of the Mods existance, they would either have to issue a Cease and Desist Order to the Project M Team or run the risk of not only losing the rights to Super Smash Bros, but also possibly the rights to all the characters/series contained in said game, none of which Nintendo would even allow to be risked