I'm far from confident that anything will come of this, though it is just suspicious enough to intrigue me.
If I were a betting man, I would bet that Nintendo doesn't have the infrastructure to stream Virtual Console games to 50 million 3DS owners around the world. Some sort of cross-buy plan, on the other hand, does sound like something they would do in time. They've been talking a lot about unifying their home and portable platforms lately. And just a few weeks ago, we got this tidbit:
“But there are some things that we’re working on that we haven’t announced here at E3 that do involve some sort of communication between the Wii U and 3DS,” Takahashi teased.
(Source: ign.com/articles/2014/06/20/nintendo-teases-future-communication-between-wii-u-and-3ds)
From the context, it sounds like they're talking about games with functionality relating to both platforms like Smash Bros, but anything is possible.