After 1600, Japan as a nation withdrew into strict seclusion. European explorers had previously reached Japan and missionaries had converted a number of Japanese to Christianity. An anti-Christian campaign was launched, and by 1640 the Japanese islands were cleansed of the western religion. That is why Swift pictures the Dutchman informing the Japanese captain that his captives are Christians. By doing so, the Dutchman would ensure a death sentence for them.
As part of Japan's self-imposed isolation all foreigners were expelled, except for some Dutch traders who were allowed to remain on the small island of Deshima in Nagasaki Harbor. This was Japan's only contact with the outside world. It accounts for the Japanese captain's ability to speak a little Dutch.
An interesting note: since Japan as part of its isolation policy forbade its population to leave the islands, and put an end to to the building of ships large enough to make sea voyages, it is highly unrealistic that there was a Japanese captain on the open seas.