Ethics of the mention of Nazi weaponry for a computational physics task
German citizen here. My feeling is that your example is not at all outrageous or morally problematic per se; but it might lead to some raised eyebrows in the given setting (a German university) and for quite understandable reasons.
You use a German WW II weapon simply to illustrate some computational problem. That is, you don't make any evaluative statement about nazism, German WW II aggression or even warfare and weapons in general. Neither is your problem about making weapons more effective, which could then be seen as an implicit value judgement.
It is also, fortunately, no longer "taboo" to discuss the nazi past. German political culture has overcome the lead-heavy immediate post-war period, in which the memory of the atrocities that Germans had committed was actively repressed together with everything that reminded of them. To be sure, there is a (perhaps large) minority that prefers to rationalize, relativize or even idealize the nazi regime and its crimes. Some of these guys have a strange fascination for WW II memorabilia and nazi paraphernalia. Here it can be hard to draw the line between hobby historians and hobby revisionists.
So as your student I would wonder: Of all the examples that you could have chosen, why this particular one? If the course was about military history or WW II, the choice of example would make immediate sense. But since it isn't, your example seems quite arbitrary. (Wouldn't other projectiles or objects have similar physical properties?) This would probably lead me to conclude that the example is "just and example", but I couldn't quite help to speculate a bit about your motivation and perhaps your historical-political attitude. Less so, however, if you are not a German.
No, his concerns are not valid and you should not abandon the project, which has scientific value as well as a small amount of historical added value that I think is of independent interest. There is nothing about the representations of Nazis or Nazi history in this project that would make it any different from mentioning the Nazis anywhere else, e.g., in a movie or work of literature, or in the Wikipedia article you linked to about Nazi weaponry for that matter. So your colleague's logic would imply that one must never discuss anything related to the Nazis, which is clearly absurd and false. Of course, an important piece of context is that you are in Germany, which leads me to speculate that your colleague has indeed been conditioned by his upbringing to shy away from discussions of Nazism. Perhaps he had family members who were involved in the war and his parents discouraged him from discussing Nazi history, or he absorbed this sentiment at school or through the media; who knows? But it is pretty clear that his sensitivity about these things has reached rather exaggerated and irrational levels.
Incidentally, warfare in general and World War II in particular have driven a large amount of development of new scientific and technological ideas. Personally I find it fascinating to read about this interaction between science and world affairs, including reading about scientific work the "bad guys" did, and fail to see how merely studying historical events can carry any moral or ethical meaning or can be anything other than a good thing.
I don't see anything immoral about it. What if the weapon was used by Americans? It's an aspect of history and if the weapon has an interesting application in your course, why not use it?
Personal feelings aside, if you're worried about stepping on your colleague's toes, you could just describe it as a generic projectile and not mention its historical significance so you can still use it in your course material. I don't know the logistics of your project, but why be specific about the weapon?