It depends on the import rules of Germany. I have a hard case and I take the dou (body with skin) with me on the airplane and let the neck be in the case together with soft clothes. Kyle has made a video on the subject on youtube.
I got my instrument shipped to me. I had to pay a lot of tax and customs fee. While I have papers stating I have paid for it, I’m sure you can just buy a shamisen in Japan and bring it back saying it’s yours or that you received it as a gift or that you made it.
When I went to Japan with it a month ago they just asked if it was a weapon at the Swedish airport. Arriving in Japan they didn’t really comment on the shamisen.
Going back to the EU was a bit different. My trip went through Finland. They wanted me to open my bag and show them. I just said it was part of an instrument and that it has skin that can break easily so that’s why I didn’t check it in. They didn’t ask me what kind of skin it was. If they would have I would just have said “I think it’s goat”, as a good enough ignorant answer. Anyways that was enough for them. I also wore our fine Bachido t-shirt, but I’m sure it’ll go smooth without it as well 
When continuing your way to Germany, whether from Finland or France, you should be able to bring it without declaring it if you want to. I know they have police with machine guns in German airports so I don’t know how much more they check there though
