When I first started playing Destiny I didn't see any of my pre-order bonuses. But once I got to the tower I noticed the postmaster had my bonuses for me. You'll notice in my inventory that you get 2 gamestop sparrows and 3 ghost casings but only 1 ship skin. This is because the pre-order bonuses are not an account wide unlock that you can have for every single character. Instead you only get a few of each bonus. So through them in your storage so any future characters you create can use the extra ones.