From the perspective of someone from Japan, I suppose there are some reasons.
First, the saturation of English names. Because there are quite a lot of anime/manga contents in Japan, it is really hard to find a new nice English name for a new character. One handy solutions is to pick a German name.
Second, the ease of pronunciation. Because Japanese language has only 5 vowels: "あいうえお", some European names are a bit hard to hear and/or pronounce for Japanese-speakers, though most German names are not really hard to pronounce.
Finally, Japanese just love Germany. They (we) have learned many things like constitutions, medicals and chemicals from Germany. They also love German products like BMW automobiles, artificial hearts, etc. and believe Germans are hard-working, honest and industrious. (Personally, I also rely on German middle-wares).
I guess past military relationships between Germany and Japan don't make Japanese love Germany, because Japanese regret WW2 and grieve what happened in Europe. Years ago, a Japanese comedian said black jokes which affirm the Axis on TV (of course, he was just joking). After that, he was heavily criticized and had to apologize in public.
Anyways today's era is wonderful because we all can talk about anime and manga here, isn't it. See you. ;)