It not going to happen because of the IP Agreement with CBS. The Dev's have stated in the past is that this limitation is present because CBS insisited that they will be no potential confilict between ship numbering in the game, and ships that have appeared, (or will appear...) in any of the Star Trek TV series....
well that jsut seems stupid. I mean they are obviousloy rebooting the franchise, and setting it in a alternate reality, I dont really think they have any plans of going back to the prime universe.
and if they are worried about using registries that are already established then they should just lock those numbers.
It is not Cryptics fault. If CBS says "No." to anything Star Trek related in this game - Cryptic has to change it. Every uniform, shipmodel, species, mission, etc. has to be checked by CBS to become the official approval. Lets remember about nine months back:
The release of the Nomad Star Cruiser skin was pushed back, CBS has rejected the design (I think it has even been rejected three times!) and Cryptic had to alter it again and again until CBS was okay with it. It is a situation which sucks for us and IMO also sucks for Cryptic, but there is simply no way around it.