So related or not, it seems very likely that the end result will be no tuition waiver for children in those schools.
Just recently, the U.N. Committee on the Elimination of Racial Discrimination, issued it's report on Japan. According to the report, things have improved somewhat since 2001, but there's still plenty of to room to go. Some of the criticism was aimed at the treatment of Chinese and Korean "nationals" such as the lack of accreditation for their schools. One NGO showed a video of kind nutjobs in Kyoto:
...waving flags and protesting aggressively in front of a North Korean school in Kyoto Prefecture, shouting phrases such as "This is a North Korean spy training center!" Japan Times: Japan faces UN...
According to that article, other members expressed concern that these schools received no "government funding at a time when the government is considering removing tuition fees for public high schools."
I, too, would like to state that the abduction issue and the tuition waiver are not, and could not possibly be related. It's a simple matter of coincidence and bureaucratic rules.