To activate the NX designation, you need to rename your ship. To do this, press U, select the status tab, and select your ship, along the bottom should be a button labeled "rename." You will see your ship's current name and your ship's registry number. In front of the registry number is a drop down box that says "NCC", click on it, and you can select "NX".
I did this, and my first time zoning my ship (graphically on the hull) no longer says NX, but NCC. If I look at the information for my ship it shows NX, and it wants to charge me 1500 to change to NCC so I can try changing it back for another 1500.
I also noticed however that same time I zoned, I lost my red matter capacitor and pre order turret... The game still thinks I have it so I can't reclaim it from the c-store... I've tried right clicking all the slots and placing things into each slot to try and find hidden items.
I've also entered a bug ticket, but much like all my tickets and GM requests between retail and live - no response.
I have a similar problem, I preordered the digital deluxe version from Steam but I dont have any of the items or the NX prefix... was I meant too put in a code, It seemed like it did it automaticly when I created the Cryptic account for it.
I got my Digital Deluxe Download from Atari.com and, as far as I can see, I have most of the pre-order goodies except for the one I wanted the most... the "NX" prefix!! I've done what has been said, but for me the dropdown to select "NCC" or "NX" isn't there!