Nintendo doesn't want downloads treated as second-class citizens.
Nintendo will not be using any special name for downloadable software on 3DS, according to an anonymous third-party developer we spoke with at E3.
Though Nintendo filed for 3DSWare trademarks, it appears the name will go unused. Apparently, Nintendo wants to remove the distinction between downloadable titles and those released on physical media. They found that many automatically assume that download games contain inferior content. By removing the "Ware" distinction, they hope to remove stigma on software appearing on the eShop.
Some WiiWare/DSiWare developers have received 3DS development kits, but there is currently no time frame for when such games might appear. The eShop launched with the first downloadable title, Pokédex 3D, last week.