sammyk,
I am not all that familiar with the Type IX U-Boat, so please forgive my ignorance, but if the deck is painted, what would it have been made from on the original? Wood? Steel?
Also, are you building the model for static display, for surface sailing only or for actually diving?
And, finally, to what scale are you building, roughly what size planks are you thinking you will need, and to what underlying material will you need to glue them?
I am of course asking the above qustion in order to better be able to form and give you my opinions in reply to your questions!
For planking a deck where the wood grain remains visible, either just varnished or stained and varnished, one of my favourite woods would be maple: it is fine-grained enough that the grain does not look completely out of scale, and I find that it strikes a happy medium between soft and hard; it is hard enough not to take e.g. a nail mark too easily (as opposed to e.g. lime), drills and sans well, but is not so hard that it becomes very difficult to cut to shape.
However, if the planking was to be painted, and in particular if it were to painted and to represent a steel surface, I would think both twice and trice before using wood as a building material unless I really had to, as you will need to apply and sand down a fair amount of filler before the grain is completely hidden. For any painted structure that should ressemble steel or a similar, man-made material, and that does not rqeuire too much structural strength, I would, depending on scale and static or sailing considerations, first look at either styrene or brass.
As for glue, that would depend on the underlying surface (wood-to-wood or wood-to-something else?) and also on how water-resistant you need the joints to be (i.e. static, surface sailing or sailing and diving?). For wood-to-wood static, any PVA glue will be fine; for wood-to-wood surface sailing, an aliphatic resin (I like the one from Deluxe Materials but there are others); for wood-to-non wood static, PVA or CA; for any wood-to-non wood sailing or diving, epoxy.
/Mattias