Been there, done that (done that so many times I care to forget it). As far as I know this is the only way to achieve that pseudo 'planked deck' finish, unless you want to actually replace the deck with a real wooden one!
While reading your post, I had a flash of an idea. If it can be done, it would save some time for future models. Here's my brainstrom suggestion - If you are able to do your own photo-etching, you could make a stencile master-template out of a brass plate. You may need to make 2 or 3 master plates. They may only be a couple of centimetres (or inches for you non-metric blokes) in area size. All you need is to remove very thin strips off the master-template at random areas. Then you spray paint the deck in various shades of deck colour, while moving the template to various areas of the ship. However, I see a couple of problems with this - 1) how do you get a template in-btw those boffins and hard-to-reach places; 2) is it hard to make the planks line up with eachother using multiply templates; 3) and is this method more trouble than it's worth.
I don't know whether this is possible, but the idea just came to me. Forget my ramblings if this seems too difficult cos it probably is!