The U.S. Navy has been fielding the Raytheon RIM-161A Standard Missile 3 for the last couple of years on a growing number of warships equipped with Aegis defense systems, and Japan is scheduled to begin deployment in the latter part of 2007. It's the missile component of what the US Navy calls the NTW-TBMD (Navy Theater Wide - Theater Ballistic Missile Defense). In other words, intended from the start as a sea-based ballistic missile defense, rather than an advanced air defense missile with some capability against medium-range ballistic missiles (like the Patriot PAC-3, which Japan will also begin deploying soon).
The RIM-161A isn't perfect, but from what I've read the results of the tests have steadily improved since the prototypes were tested in the '90s. Would it make the North Koreans think twice about launching an actual missile attack against, say, Japan? Maybe. I don't think they're likely to do something that insane anyway because they know what the US reaction would inevitably be. But if they knew that the US and Japan had an ability to shoot down, say, 60% of their missiles, yeah, that very well could be enough to deter them. In any event, the US currently has some missile defense capability in the Pacific, and Japan will as well in the not-too-distant future.