I've been told that they'll never do this with guitars, but...
...apparently all it takes is an agency's "order" to ban the import of all ivory regardless of age or context, such that an antique upright piano is now stuck in Japan, apparently forever. I'm pretty sure none of my old guitars has ivory pins, but if they did an order like that for rosewood, it would (effectively, probably) ban every single one of my old, beat-up, but very lovable electric guitars, since there's no way of proving or even knowing the source of their rosewood fingerboards. Also, I'm not even 100% certain that such an order hasn't already happened, and I don't really know how to go about finding out whether or not one has. I assume if it were to happen it would make the news, but, you know, maybe I'd miss the news that day, or I could be the first.
This woman had no idea that buying lobsters in plastic bags would put her in prison for eight years, and there was no way for her to "check" even if she had thought to wonder whether putting lobsters in plastic bags was illegal, because the government that prosecuted her didn't know itself till it had done months of research to find something, anything, to charge her with. I guess there are two kinds of people in this world, those who see a story like that and think "well then, I'll just avoid lobsters in plastic bags from now on," and those who think "if it could happen with lobsters it could certainly happen with guitars."
Anyway, I'd really think twice about bringing a vintage guitar to Japan, or anywhere foreign at this point. Maybe get a new, travel-only guitar, keep it "clean" and keep all the documentation, like they advise you to do with laptops. Having to prove your innocence is hard enough for a human, but a dumb guitar really doesn't stand a chance.
(Also pre-order my book.)