Hi Nick,
I would say that most merchant ships had minimal colors used on them because colored paint was expensive and not something they would want to spend money on. Most would probably have been painted black with perhaps some white or tallow in the paint scheme, especially the lower hull. I doubt that stains were in use at that time. If you do a search in Google for "merchant ships 1700 images," you'll see photos of replica's and drawings of some merchant ships to get an idea of the colors used. It might also depend on the country of the ship as well.
Bob