The system firmware will update out of the box for eShop support. UPDATED with NOA comment!
Nintendo of Europe confirmed to Eurogamer that while the eShop and Internet browser functionality will not be pre-installed on the firmware for launch systems, it will be released on launch day as a system update.
Nintendo's 3DS preview event revealed that an Internet browser and eShop featuring DSiWare, 3DS download titles, and Virtual Console Game Boy/Game Boy Color would be part of the Nintendo 3DS functionality, but they would not be a part of the system at launch. The features would be installed through a firmware update available during the "launch window."
It is expected that Virtual Console titles Legend of Zelda: Link's Awakening DX and Super Mario Land will be available once the eShop is active.
UPDATE: NWR contacted Nintendo of America for an official comment. NOA's Senior Director of Corporate Communications, Charlie Scibetta, had this to say:
“Games and services offered by Nintendo can vary by region. Nintendo of America will release additional information about Nintendo eShop, including timing, content and pricing, at a later date.”