Craig Zinkevich said himself that it will take a looooooooooong time for them to add it to the C-Stor. And that is IF they decide to add it.
It would be extra $$$ for them when or if they decide to add it to the c-store.
My opinion, which does not matter one bit I might add, would be that all items which were featured in any of the TV or movies should be available to all at some point in time through the C-store, although at least not for awhile.
Yea, from what I've been told, some pre-order bonuses may end up there eventually a ways down the road.
CE bonuses, however, will never be put up for sale as it devalues the Collectors Edition, which normally increase in value over time. A WoW collectors edition can be sold for over $200 on Ebay, and if STO will ever see such a thing they have to keep CE exclusives... exclusive.