For the same reason they didn't for the most part have iron nails...it rusts! the best wooden ships were made with wooden pegs, and mortice and tenon joints. the seams were sealed with oakem (made in Dickens' time, at the 'work house', by poor homeless folk, in return for what we would now call welfare or the dole) Oakem is wood that has been pounded into threads.
a bo'sun was lowered over the side of the ship to pack oakem into the joints, and seal them with hot tar. small leather or canvas seats, raised and lowered by ropes (used by workers building the Hoover Dam, and by rock gardeners) are still called bo'sun seats.
The metal tools used by the sailors, all had leather thongs, and would be worn on the wrist, so if they slipped from the sailors hand, they would not sink. Wooden mallets, if dropped, would float.
