For anyone who cares to have the proper German and Japanese flags within the game, these below files will accomplish that. Be sure to backup the respective files prior to copying these new files over (<Install DIR>\GFX\map\flags and <Install DIR>\GFX\map\shields DIRs -> Look at the file structure of the archive to determine files to backup). There's only 4 total files, so it shouldn't be a big deal to anyone. Enjoy!

http://www.mediafire.com/download/bb8noecrzqnb1c3/HOI_Historical_Flags.zip

I can guess why the German flag got the historical negationism treatment, but why the Japanese flag?

Japan was Imperial prior to and during WW2. Post-WW2, perhaps the rising sun flag was associated with the fall of the idea of the Emperor being the "voice of God", and Japan adopted the newer flag to signify a new era. Paradox probably just didn't want to stir up any animosity regarding it.

More info :
https://en.wikipedia.org/wiki/Flag_of_Japan