Earlier quoted context omitted.
Japanese Twitter tells me that once this station closes, there will be a 40 minute section of the railway that won't have any stops. The line itself will remain operational.
Looking at Google Maps the change won't be terribly drastic in reality [0] unless the station just over 3 km further down the line closes too. For a person walking it's a decent distance but for the rest of the passengers there would be very little change. Of course the same could be said for pretty much any station that closed between there before now. [0] https://goo.gl/maps/cqZBrzvjJJk
One possibility is that the station 3km away is already out of operation (and I do recall someone posting that a nearby station did already shut down).
In either case I think you are right that for 99% of the passenger life will go on as it always has.