On this issue, the Supreme Court held that the freedom of news gathering for the news report deserves sufficient protection in light of the spirit of the (Japanese version of) First Amendment, in In Re Subpoena against RKB Mainich Broadcast Co., 23-11 Keishu 1490 (November 26, 1969). However, that does not mean that anything journalists do would be justified.
I already posted on one old case where a journalist who had a sexual relationship with a government official to obtain secret information was convicted. Further, in another old case, a journalist received a piece of important evidence from a criminal group and eventually burned it up (allegedly, to avoid being confused as a group member). The prosecutor accused him and he was convicted in People v. Doe, 703 Hanrei-Jiho 121 (Urawa District Court, September 27, 1972). The court stated that it was regretful that the journalist approached the information source without consideration and made intimate connections which resulted in him assisting the criminal group.
Relatively recently, two new cases were held. Although they do not directly deal with typical journalists, they are somewhat relevant. One case is an environmental protest group case. Group members, who wanted to investigate and report allegedly unlawful whale-hunting stole a piece of whale meat. Although they argued that it was necessary information gathering, the court did not buy the argument. The court held that even an investigation for public interest cannot be justified unless conducted so as not to invade other people's freedom and rights, and convicted them. This was an unreported case of Sendai High Court on July 12, 2011.
Another case is that a journalist approached a doctor who was appointed as an expert on a high-profile criminal case and had some secret documents of the case. The doctor lent her the documents and later she wrote a book using the information. Both the journalist and doctor were arrested but only the doctor was prosecuted and later convicted. Nara District Court stated although more deliberate and careful review was necessary in the case of journalist, as the doctor accused was only an information source, the level of scrutiny is different and was thus denied justification. People v. Doe, 2048 Hanrei-Jiho 135 (Nara District Court April 15, 2009). The conclusion of denying justification is affirmed by the Supreme Court in People v. Doe, 66-44 Keishu 405 (Feb 13, 2012).
As of now the information is scarce, and as a result, I cannot say whether the acts of a journalist "hacker" are justifiable. But three things can be said. First, prosecutors seem to respect the freedom of the press when they exercise their discretion on whether to accuse a suspect. So, there is a possibility that the prosecutors will decide not to accuse the journalist, like in Nara's secret document case. Second, once a journalist is accused, the chance of acquittal might not be very large considering the courts' attitude in two old cases. Third, the defense should focus on the distinction Nara District Court made (and Sendai High Court might have made implicitly) between real journalists and others (such as information sources or activist groups). The defense counsel can emphasize the fact that the journalist belongs to a reputable news service but, as I said, I am not sure whether this line of argument acquits the journalist.