I've purchased a few items from Japan myself. Mainly some Nikkors and accessories, etc. No problems. My main concern is with older bodies, like Nikon F and F2 bodies that have had time to live in the humidity. There have been a few F2 bodies that look real nice and clean that have been sent to Sover Wong (soverf2repair here) and are covered in mold inside. An F4 or F5, no problem. New enough that it probably won't have fungus. Or, if it does, it'll be something that can be cleaned off with Windex.
That said, if you do decide to have Nikon service it, they will be looking for either the "US" stamp on an F4, or the little oval "NikonUSA" sticker on the flap covering the buttons on the rear of an F5... Not that big of a deal with an F4, since, if the wind-side top cover is iffy, find a junker in the states with a better one, and swap it. Then, send the camera in. From what I've read, Nikon USA won't service anything gray market, even if it's out of warranty. Most independent shops won't care. I'm guessing my father sent his Nikomat FTn to a local independent shop when it got dropped in the early '70s. That would be why his camera wound up being cobbled together with different versions of the FTn, parts-wise. 361xxxx serial, but meter coupling that went to f/32, and an AR-1 compatible shutter release button assembly, as well as the newer takeup spool.
I've yet to have to pay duty on overseas purchases, even on the two F3P bodies I bought from the UK (one around the time I joined here, and the other in the summer of 2013). Just had to go into the lobby, show either the yellow or small beige sheet of paper, sign/print my name, then print the delivery address. After that, my parcels were passed over the counter to me.
-J