I don't know what the english manual looks like, but in the german manual on page 18 (there are some facts about ships) it states (and this is translated text into english!):
Because ships are equipped with "Paperdoll" inventories (graphical designs of items, which can be equipped on a ship) and bridges, your decisions will have an impact on your ships weapons, impulse engines, shields, deflector srrays and modifications [...]
If I did not interprete that wrong, that sounds like your ship can look different if you equip lets say a tachyon deflector and after that you change to a normal deflector array.
But while ingame, I was not able to see such ship customizations until closed beta!
Is this really working as described in the manual (if yes I am kinda blind), or is the manual lying here?
There are graphic depictions of items. They can be drag/dropped into slots on the ship equipment page. These items do change the behavior of your ship. I don't see anywhere in that quote that they will change the appearance of your ship.
I haven't played the game yet, but what I can tell from that text is that the ships will have a paperdoll "character" sheet, where you can equip items on it that will change the effectivness of your ship. Doesn't say anything about changing the looks of your ship though.
Although can't you customize your ship through a different window? (seen that on a video)