According to TG Daily, Eiji Aonuma confirmed that The Legend of Zelda: Phantom Hourglass will include online multiplayer battles.
In an interview by Game Informer Magazine, Eiji Aonuma answered a simple “yes” when asked if Phantom Hourglass will have online play. This will make PH the first Zelda game in 20 years to have online play and if you exclude BS Zelda it would be the first. The wait for this game just get more and more tedious.
Also, check out the full Game Informer Interview here.