onxyman is correct, Chris Freidenbach (sp?) a crewman on the real Jeremiah O'Brien, gave an exhaustive rundown earlier this year of all the little things you have to do to make a truly accurate model. You MIGHT be able to find it by doing a search.
When I was building my 1/700 resin Victory ship I had another consultant, my Dad, who served on several during the war. He said that while the ships were usually a gull or haze gray shade, the decks were sometimes a darker gray, like modern US Navy ships, but sometimes the entire ship was the same color - it just depended how much paint and what colors they had on hand when they started painting. And you know how they paint a deck in the merchant marine? Easy! Get a 5-gallon can of paint, kick it over, and go at it like dervishes before any runs into the scuppers and down the sides of the hull!
As for the canvas hatch covers, they do provide some color. Dad remembered them as being a rusty or dirty brown, but I opted for a newer look by using a green, based on what Christ Freidenbach said. I went through a ton of greens at the hobby shop, and finally settled on Model Master RAF Interior Green, #2062, as looking the most like newer canvas circa WWII.
There are other "spots" of color - the firehoses will be off-white with a brass nozzle on the end, and a flat red curved holder; fire hydrants were commonly red; life rings could be either white or gray, depending on who was doing the painting that day; the ship's name board would be flat black with white block lettering; the various running and navigation lights would provide points of red, green and white; deck cargo crates can be many different shades of tan and brown; you get the idea. When I modeled the LaCrosse Victory that my Dad served on, I included a deck cargo of Sherman tanks that he remembered from one trip, along with cargo crates and oil drums in various shades of black and green. Add a few crewmen in their dark blue dungarees, blue workshirts and white hats, and it's more than enough to break up the mass of gray ship.