Has Nintendo ever mentioned releasing games for Virtual Console (or whatever) games that were previously unreleased, such as Star Fox 2 (SNES) or any others? Moreover, has any company ever released any beta versions of games long after they had hit the cutting-room floor?
Yes, Nintendo has indeed released previously unreleased games through Virtual Console. One of the most prominent example would be Mother, which was released in Japan only in 1989 for Famicom (aka NES in the West) and 2003 for GBA.
It is said that the game had already been translated into English, but due to the newly released SNES, was never released in the West. Instead, its successor, Mother 2 was released for SNES in the West under the name: EarthBound.
In 2015, the game finally made it to the West under the name EarthBound Beginnings on the Wii U as a Virtual Console NES game.