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I've just read Japan Keeps This Defunct Train Station Running for Just One Passenger, about a station that'll be closing this year (2016) because its last user, a high school student, will be graduating.
When they're abandoned, are train stations demolished, or allowed to just decay? And is it possible to either get to them, or at least go past them, via public transport?
Depends. It's kind of unusual for individual stations to be taken out of service (unless they're building a replacement nearby), but Japan has lots of abandoned train lines and, thanks to rural depopulation, lots more on the way.
There are three basic possibilities:
Demolished. Usually happens when there is some other sensible use for the land: for example, the spot where the Ofuna terminus of the Yokohama Dreamland Monorail once stood is now an apartment block.
Repurposed. Rare in Japan, alas, but happens on occasion if the building has some architectural value and some use. For example, the remains of Manseibashi station in Tokyo are now a shopping arcade/office complex.
Left to decay. The typical fate of small, rural stations that never had much meaningful infrastructure in the first place, meaning there was just a platform, a sign and a mouldering shed.
For practical examples of each, this rather interesting video blog series documents the cycling trek of a couple of intrepid Westerners along a series of abandoned railway lines in Hokkaido, Japan's most rapidly-depopulating island. Check out the trailer for a sampler.
When service to a single station, as opposed to an entire line, is discontinued as in the case of Kami-Shirataki station, the trains which used to stop there are still running, they just no longer make that stop. So it's possible to "pass by" the station by simply taking those trains.
Whether it is easy to actually go to the station obviously varies, but your best bet is probably to take a train to the nearest (still operating) station on the line, and walk to the defunct station, as it is unlikely that bus service to that station will be maintained. If the station is near a population center, however, there may be some bus service to a nearby place... Every case is different. In the case of Kami-Shirataki station, it is "only" a couple of kilometers from Shirataki station, which has much more frequent service (it is even served by Okhotsk limited expresses).
Of course, if the entire line is being discontinued, buses are most likely the only public transport option (if they exist), but it is also possible that there is another line which has a station nearby (that would be more likely in urban settings).
Usually, the building is left, but here again each case is different, it may be destroyed (if there was a building at all...) if it poses some sort of risk.
