Marcel,
The weathering isn't too difficult to make. But as usually you have to remember about the model scale. In other words the weathering effects have to be of the same scale. As a result some of experience and practical skills are needed. Making of such effects on models with raised panel lines isn't a good idea often because you may get just a dirty model instead. Therefore making of the weathering should be planned much earlier. For instance, before attaching turrets , quarter-decks, etc. It makes our work easier. Well... to answer your question... I would let the deck as it is now. Later, when the main block of the model is almost finished, we may have a look at it again and decide if there is any possibility of the weathering applying. I would wait, in my opinion.