Nintendo Australia issued a statement on the rumors that GBA games would be coming to the 3DS Virtual Console service:
Nintendo Australia would like to confirm the recent update to the website highlighting Game Boy Advance titles are available on Nintendo eShop was posted in error. Nintendo Australia can confirm there are no current plans for Game Boy Advance games to be released on Virtual Console for Nintendo 3DS. We would also like to confirm Dr. Mario is available as a Game Boy title on Virtual Console via Nintendo eShop. We would like to apologize for any confusion this has caused.
My take: Sounds like damage control to me. Someone probably screwed up.
Source: GoNintendoLabels: 3DS, Game Boy Advance, GBA, Nintendo 3DS, Portables, Rumor Updates, Rumors, Virtual Console