See, it's this kind of reply that just makes me shake my head. To start, Nintendo has had virtual console on three different systems (Wii, 3DS, and Wii U). They have the data for the profit margins of those services compared to the licensing and other fees. Clearly it wasn't incredibly profitable, otherwise we WOULD have those services. Instead they've gone a different route: subscription based services. They are now using these games as an incentive to get people to subscribe to their network fee. They've been trickling in games to maintain interest (hence why they actually had to add games like Donkey Kong Country instead of having everything available from day one).
As for why there aren't games like Earthbound and Mario RPG, to start their are parts of those properties that aren't wholly owned by Nintendo. They may have to pay royalties to certain individuals. Characters that were created by an individual need to be accredited, and especially music from composers. For Super Mario RPG, Nintendo might not even have complete ownership of that IP as, from what I understand, Paper Mario is, in part, not called Super Mario RPG 2 due to legal issues with Square Enix (Squaresoft at the time).
Even if the above ISN'T the case, people are more likely to resubscribe to a service as more content becomes available. For example, someone may have subscribed for the Donkey Kong Trilogy, even if just for a month, then cancelled once they were done. When/if they announce Earthbound that person might subscribe again just to play that game. Maybe it sounds silly to you, but it's certainly possible.
In sum, yes Nintendo absolutely knows what they are doing. They are the most consistently profitable gaming company out of the three even when the others are getting SIGNIFICANTLY more revenue. Their decisions are calculated. If this subscription model turns out to not be as profitable as their Virtual Console business you can bet they will bring that back.