PC game communities show pretty well that if devs support the mod community, then they gain more from the same game than if they shut down mod projects (though in the case of PC games, you don't have to really worry about ended distribution for games, and most devs could care less about post-life piracy if they haven't kept their game in circulation of their own accord). There's virtually no reason to support past games at all if they're simply trying to support Smash4. If they're trying to support the series (not like they're even capable of making more money off of Melee and Brawl, since they're out of print and aren't available on Virtual Console), then supporting all versions, official or unofficial, is the most reliable way to do that.
Unfortunately, Nintendo gets really antsy over their intellectual property no matter what you do with it. I wouldn't expect them to support Project M, but seeing as it's a darn-near professional-quality mod of a AAA game, I would really hate to see it fall off just because Nintendo chokes it out of major events by sponsoring 'em (instead of just C&Ding it if they're really against it. I imagine if they really were trying to kill PM, they'd have done so months or years ago).