Hi Jacob,
Officially the wooden flight deck color for US aircraft carriers during World War Two was universally Flight Deck Stain 21, a shade close to the 5-N Navy Blue of the hull and superstructure of many ships. However, busy combat schedules usually precluded careful maintenance.
The following photographs of the Enterprise taken in the Spring of 1945, show the blue stain she wore at this time almost completely weathered away:
Here’s an image from another source, this one a capture from a movie that was shot aboard Enterprise moments after the 14 May, 1945 Kamikaze attack showing sailors evacuating a casualty:
http://www.criticalpast.com/products/search/?sort_order=asc&q=cv-6&page=3It is hard to know how much to trust reproductions of old color photographs or movie captures, but comparison of the deck color with the dark blue denim trousers and the lighter blue chambray shirts on the sailors suggests that the deck has in this case weathered to a mostly brown color.
On the other hand, more recently stained flight decks would appear a very pretty, neat blue... so you have a choice!
