Subfixer is right - generally speaking. There were some exceptions (the decks of the battleships at Pearl Harbor on December 7, 1941, for instance, and the decks of aircraft carriers were treated with mahogany stain before the war started), but generally speaking the typical wood deck during the war was stained either grey or blue.
There are, of course, plenty of other occasions for simulating an unpainted wood deck. (Come to think of it, was there any other period in naval history when unpainted decks were
not the norm?) Different kinds of wood have been used for deck planking over the centuries, and different species have different colors. Pine, fir, and teak have all been used for deck planking, and all of them look different when they're freshly-laid.
My own opinion, for what little it's worth, is that unpainted deck planking, especially after the sun's shone on it, salt and rain water have soaked it, and human beings have stomped on it for some time, is considerably more grey than brown in color. The value (i.e., darkness) of it varies considerably. It's interesting to study black-and-white pictures and note whether the deck planking is lighter or darker than the painted surfaces. (Warning: if the deck has recently been hosed down, or rained on, all bets are off.)
The old Poly-S line of latex paints used to include a color called "Sahara Sand" that, to my eye at least, looked just about right: a medium, nodescript grey with a beige tint. That color isn't made any more. Poly-Scale does make a color called "Weathered Concrete" that comes pretty close - though I'd like it better if it had just a touch more brown in it.
The bottom line is that this is one of those areas of model building that allow for some personal taste and judgment.