Yes, matte is really the opposite of what you should do, it should've been glossy. Then, after the wash, make them matte. I've never painted a ship, only 1/285 planes and 15mm tanks and soldiers, but I think that after 2 matte coats, a further gloss coat and a final matte coat again would cover up some fine detail and make your ship less angular and crisp, and more gooey-like.
However, you could still apply the wash selectively, as opposed to brushing the whole ship with a fat brush of wash. Take a small brush, say a 0 size, and paint the wash on more part by part, following the crevices with the brush. The stack, the bridge, the turrets, area by area. Each window and each line one by one. That way, you keep the darkening only to the nooks and crannies :)
As for what color, I'd say plain ol' black. Black is color-neutral by definition: "the absence of light". Adding blue ink will accentuate the blue-grays, but "blueify" the neutral grays, dark or light. The ship WILL look awesome regardless, but it's your call :)
Maybe try each formula on a lowly destroyer apiece, and then select the winner for the rest of the fleet ;)
Rolando