In what sense do you mean? If you mean has it ever been done at all? Then yes I can pick one off my shelf that does. Black Lagoon in this case has a story arc involving Nazi artifacts and flashes back to WW2 for it. I can remember several others off the top of my head and they all treat Nazis similar to Western depictions, that is when not farcical as being generally evil.

Osamu Tezuka(the "father" of modern manga) also did a series called Adolf that is set in Nazi Germany. This was made in the 80s. There was also an anime adaption of Anne Frank's diary released in the late 70s.

So to your question as phrased the answer is yes, quite a bit as it happens. But perhaps you were asking about a more specific time period or about Japanese attitudes towards Nazis, in which case I suggest resubmitting with less.broad phrasing so that someone with expertise on Japanese culture might be tempted into answering.