I initially thought the same -- getting them is a bit convoluted...
You have to go to the C-Store in-game. The icon for the C-Store is located next to your mini-map in the upper right hand corner. Find the icon by pressing the "down arrow" and selecting C-Store...when the C-Store opens up, you will see a tab called "Special Unlocks". Your gear should be in there. You have to select each one and press "Claim."
When I first did this for the Enterprise pre-order bonus, I could not initially find my ship...but then I found it amongst the clutter of my inventory -- you double click on the item in your inventory, and the ship will appear in your ship list.
If you went through these steps...and your stuff is not there, then it is time to get ahold of technical support -- they will sort it out for you.