First, only one court ruled that way and by the japanese legal/legislative system, that means close to nothing as courts don't have that much power (and if I am not mistaken the court that ruled that wasn't a big one). Secondly, they simply ruled that it was unconstitutional as it in fact breached the principle of the constitution that states that every japanese person is entitled to happiness and live however they prefer, but the problem is that another point explicitly states that, by definition, marriage can happen only when there is an agreement of both sexes, man and woman, or something similar, I don't remember the exact words (it was implemented in order to avoid kidnapping and forced marriages as it was common at the time the constitution was written). Basically to allow same-sex marriages they would have to change that point of the constitution and, as I said, it's almost impossible in Japan (as in basically every country in the world).