Can one find out if somebody naturalized from their legal Japanese ID?

When people learn I'm a Japanese national, they naturally (and correctly) first assume, from my very non-Japanese appearance and because I speak Japanese with a slight non-native accent, that I was neither born nor grew up here.

South Park creators parodied the
Native American / Japanese
conspiracy theory in
"Cannibal! The Musical"

So their follow-up question and assumption is often about how or "why" I am Japanese. Laughably, I have had many people ask if I was ハーフ {hāfu} (mixed race), even though there is absolutely no DNA affecting my phenotype that should give people that idea. U.S. Senator Elizabeth Warren is probably more Native American than I am Asian. They ask this question because most Japanese and non-Japanese have met people who don't appear to be Japanese yet are, and the most common explanation is that their in Japanese ancestry in their lineage.

There actually are Japanese people who were born in Japan, grew up completely in Japan, and speak only Japanese with such flawless pronunciation, vocabulary, and grammar that they could work in their field of broadcast communication or studio voice over work — yet from a physical "racial" aspect, are completely and obviously non-Asian (ex. visibly pass as White or Black).

So to posit the question: if you "look Asian" and you speak flawless Japanese and have the same knowledge and experience with Japanese culture as somebody that grew up exclusively in Japan, could somebody discover you have naturalized from examining your day-to-day use legal Japanese identification?

And the short answer is: no.

The long answer is: there is one document, the unabridged family register (戸籍謄本 {koseki tōhon}) that indicates you naturalized, but this is not a document that is used for identification or for day-to-day life (ex. applying for employment or a bank account). And in the unusual case that you do need an official copy of your family register, you can have an abridged version issued which does not have any information about other nationalities you may have had or relinquished or renounced.

One commenter on the internet assumed:

It is my understanding that unless you are a “native” (or say, indigenous) Japanese, any identification that you carry such as your passport, will have an indication that you’re a legal citizen of foreign born in order to differentiate from the “native”. I’m saying this because this was a big political issue in 90’s. Back then, even with the Japanese passport a person has to stand in different line when they go through the custom in the airport due to the fact that you’re a foreign born.

No birthplace or "non-native" marker is present.

This understanding was false back in the nineties, and it is false now. In fact, Japanese passports, unlike the passports of other countries, do not indicate where you were born. They list one's "本籍 / Registered Domicile", which is always in Japan.

Some countries with lax or virtually non-existent naturalization standards (the countries that offer passports for cash), such as St. Kitts and Nevis, have had to recently add a birth place field to their passports so that immigration inspectors can differentiate between citizens whom the country has actually vetted and has strong ties to and CoCs: Citizens of Convenience holding "Passports of Convenience".

Like Japan passports, some Philippine passports
do not specify a specific town or city. 

I have had passport inspectors confused the Registered Domicile (本籍 {honseki}) field on the Japanese passport for my birthplace, asking when I was "born" in "Osaka" [sic]. This is because this field, which only indicates the prefecture (都道府県 {todōfuken}) and not the specific city, is unique to passports issued by Japan, and it is much more common for passports to indicate one's birthplace.

It is true that an unabridged Japanese family register will indicate if you are naturalized, have chosen a nationality, have acquired or gotten rid of foreign nationalities, but this documentation is only in the vital records section of a municipal office and is not public information; only direct immediate family members (ex. your legal spouse and immediate family), proven with legal domestic photo id, can access it — and most people do not carry it on their person (it's like a birth certificate).

There were privacy and discrimination scandals in the late eighties and early nineties, back when understanding of privacy protection was still primitive, where some companies would pay third party agents to illegally access these records (to discriminate and see if somebody was divorced, was born in the bad part of town, etc), but the government has since clamped down on privacy protections by requiring photo id in the modern era. Surprisingly, a Japanese not having any government issued photo id (ex. a passport or driver's license) was not uncommon a few decades ago, and it's still not that unusual today.

Japanese naturalized nationals, or anybody else with Japanese nationality, has never had to stand in a separate line at the airport. There ARE special queues in the CIQ for legally foreign (nationality … meaning not having a Japanese passport, not race/ethnicity) residents, which is different from the line for tourists.

There is also an additional special line for foreign residents of Japan.