First I'll note that the Dutch word used on the form is verblijfsvergunning. It is a bit difficult to answer this question, because depending on the context vergunning may be translated into English as either permit or permission, so verblijfsvergunning could refer either to a tangible document or to the intangible authorization to reside.
Still, I would I would answer "no," on the assumption that the sense the form employs is the sense that denotes a physical document. This seems a safe assumption for three reasons:
It should be common knowledge among Dutch government functionaries that Dutch citizens living in other EU countries do not require a residence document, so a negative answer to that question should be unexceptional in your case.
A Dutch citizen applying for a passport or ID card in Germany is required to show legal residence in Germany by other means than a residence permit. Specifically, you must present "een uittreksel uit het bevolkingsregister van uw woonplaats, een Erweiterte Meldebescheinigung mit Angabe der Staatsangehörigkeit" ("an extract from the population register of your place of residence, an Erweiterte Meldebescheinigung mit Angabe der Staatsangehörigkeit"). (The source of this information is Paspoort of ID-kaart aanvragen als u in Duitsland woont.)
I may be out of my depth here, because I am not a native speaker of Dutch, but I think that if the intended sense of verblijfsvergunning were the intangible sense then the question would be without the indefinite article (Heeft u verblijfsvergunning?).
I suspect that in practice your application will be successful regardless of the choice you make in answering this question.