Chiming in a little late here. Thanks to
@maryorellana and
@indojindesu for bringing this thread to my attention!
I've done a bit of research on that particular government directive and the fallout. (Please pardon me if the answer gets long and rambling).
The short version is that you have nothing to worry about. I have seen no effect on MEXT scholarship awards in social sciences and humanities. The whole issue turned into a major embarrassment for the Abe government, and they've publicly tried to clarify several times.
The source of all the news articles you saw was a government directive to national universities that directed them to consider closing or reforming
certain programs within the humanities and social sciences in their next mid-term plan.
The directive specifically targeted: Law Programs, Teacher's Training Programs that did not include earning a teaching certificate, and Economics Programs.
You've probably seen the wording that the article specifically targeted these fields because it said "universities should focus on fields that were more useful to society." Japan has an overabundance of lawyers, a teacher's training program that doesn't lead to professional certification is essentially useless, and economics . . . well, my theory is that Abe was sick of first-year undergraduate students who were smart enough to realize his Abenomics plan was doomed to fail.
These three fields were branded as not useful enough in their current form to worth national universities pursuing the. With the exception of Economics, I think there's a valid point in there. They do need reform.
Unfortunately, this got interpreted, especially in English, as "Universities should shift away from all social sciences and humanities because they aren't useful to society."
Fortunately, this misinterpretation lead to a huge blowback from Japanese universities and business. Business organizations said that they need
more social science and humanities graduates - that those programs do meet the needs of society (social science graduates from my university have 100% employment rates over the last 4 years). Some university presidents also went to bat saying that humanities and social sciences had more value for society.
In general, the social sciences and humanities got a lot more staunch, public defenders than they had had before.