Did you add the names to the Names.cfg file after installing the package? This is not done automatically, as it would mean that the current file would be erased - thus, when new ships are released both for SHIII and SHIV, modders (including me) usually provide the entry for the appropriate .cfg which is then entered manually by the user (using any work-processing program). After this is done, the lettered names shouldn't appear in the game itself anymore - those should only normally be a concern to the program itself and to modders.
BTW - They aren't necessarily acronyms, as some of them don't really stand for anything.
