The embassy might have info on modern flags, but probably not on historical flags.
The most reliable source is the considerable number of maritime paintings from the 17th century. Google images of some of the more prolific maritime painters, like Van de Velde, Backhuizen, Nooms, or Beerstraaten.
Individual captains took considerable liberty with the display of ensigns, occasionally flying the flag of the province which provided the ship to the fleet. Some of these are pictured here:
flagchart.net/provinci.htm
Occasionally, especially if the ship was named after a particular municipality like "Wapen van Delft" the flag of a specific city would be displayed. The third set down on this page has several examples of old city flags:
flagchart.net/gemeente.htm
You can also check out individual provinces or place names on the Flags of the World site:
crwflags.com/fotw/flags
Builders of large ship models occasionally display flags on their models. These craftsmen are pretty meticulous about details, so you can probably rely on their choice of ensigns. There are some good examples here, on the Model Ships page:
link
Regards,
Jeff