Most shipbuilders, if they could get it would use teak for the decks instead of softwood and I see no reason to think that the German U-boats would have been any different.

The problem with most softwood for the decks, and this would be especially true of submarines, is that over time, it gets waterlogged and expands. It then gets very slippery, especially when wet and would be very dangerous for anybody trying to walk on it.

Teak, on the other hand, is a standard for ship decks for centuries because it has excellent weather-resistance and is less slippery when wet of almost any other kind of wood that could be used.

As far as colour goes, teak can range from a reddish-mahogony-like colour to a very dark brown or a golden-honey colour when new, depending on the type of teak.

I doubt that the Kreigsmarine would have painted their teak decks since paint actually makes them slipperyer when wet and with the pressure of the water at depth, the paint would have lifted off in short order anyway. To keep the anti-slip charactaristics of teak, it would be plain, unvarnished and unpainted.

What is likely the cause of the opinion of the grey or even black colour of the decks is that without frequent sanding, the teak will quickly change colour on its own, especially if exposed to salt water. What better place for this to happen than on a submarine! It will first go light grey and then darken with age until it might sometimes get to be almost a charcoal colour. This can be removed chemically or by sanding so a boat with any damage to it would show fresh wood where it's scarred.

As far as plywood goes, I can't imagine using even a modern marine-grade plywood on a submarine deck, let alone the kind they had in the 1940's. The glues just were not good enough to stand up to continuous immersion in salt water and if the water was under pressure, it would be even worse.