The American occupiers of Japan wanted to break the power of the old Militarists. The main opposition to the Militarists were the Communists and the Rural peasants. MacArthur did not want to strengthen the Communists thus that left the rural peasants. Thus the disparity is the districts in favor or rural areas over more highly populated Urban Areas. This has become worse since the end of the occupation as more and more people left the rural areas and moved to the urban centers.
I first read of this problem in the 1970s but the party in power then and now would suffer the most if the borders were redrawn. Thus no redrawing in the 1970s and no redrawing today. Remember while Japan was a multi-party state, The Japanese Liberal Democratic Party, that party has dominated the Japanese Diet since WWII except for just a few years (The Liberal Democratic Party has ruled Japan since 1956 except for the years 1993-1994, 2009-2012).
On top of this the largest single party by votes in 1947 had been the Japanese Socialist Party. It is now a minor party, but may come back. The US did not like the fact it was the single biggest vote getter and thus supported the development of the Liberal Democratic Party. One side affect of this is that since 1947 the Courts of Japan has either been appointed by Americans (1940s only), appointed by Japanese Politicians who themselves were under strong US pressure OR appointed by the Liberal Democratic Party (LDP). All three groups opposed the Socialists and supported the LDP or groups that made up the LDP).
Thus the Court is being asked to ruled that the people who appointed them to the position of Judge were themselves unconstitutionally elected. i.e. the people they deal with on a party basis had no right to appoint them to the bench (Or select them for promotion to the bench, for Japan is a Civil Law Jurisdiction and lower judges are promoted upward either by politicians or other judges depending on the system).
In many ways the Civil Law System is more independent of Political pressure then the Common Law in that Judges tend to pick other Judges, but such selection often have Politician overtones that go back to who is in power in the Legislature.
Side note: The Civil Law System is also based on legislative supremacy, i.e. What ever the Legislature does is constitutional. Most Civil Law Courts can NOT rule a law violates the Constitution. In those Civil Law Jurisdiction that do permit a Court to strike down laws passed by the Legislature it is often a special court that hears such cases, and even then its powers are restricted. Japan seems to be the later. i.e its highest court can rule a law unconstitutional, but it is reluctant to do so even if the law clearly violates the Constitution. Thus the wording of this opinion, the Court thinks the law in unconstitutional, but instead of so ruling, is telling the Japanese Diet to repeal it instead. Not requiring such an repeal, but recommending it.
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