All the boats always had wood for their decks. You just can't tell it from the pictures because it's covered in a thick black preservative which became a charcoal color upon exposure to the elements. There were metal sections at the extreme stern and bow sections, but under preservative and paint you really can't tell they are made of different materials, even sitting right next to each other. So don't shy away from the brass kit because it's metal and the decks were wood. The pictures of U-boats do not show wood grain, and brass affords an unparalleled level of detail.
Another nice thing about brass is that it's very close to the correct thickness in scale, where the Revell deck is much too thick. In scale, the brass deck is 3/4" thick, very close to the real thing. When you look at the slots in the deck, they should actually be very thin, looking very sharp. The Revell deck shows sidewalls in the deck slots that if scaled up would make the deck way too thick, maybe 3-4". This thick look is of course a limitation of injection molding technology. The brass has the correct look of a very thin plate, which is how it looks in the pictures. It's the same story for the holes in the sea hull, both limber holes and flooding holes. The sea hull should be quite thin, and all holes that go through it should present as thin a profile as possible.
The late war VIIC had a much simplified deck which is more recognizable as wood since it's installed in long parallel slats. This is the boat with the double wintergarten and the row of cannisters toward the bow.