You'd think that would have been considered. The miniatures made for the DS9 Tribble episode ought to have still been in Paramount's hands when the remastering started. Other ships like the Fesarius and the Doomsday Machine could be CGI.
Personally, I would have borrowed the original big E back from the Smithsonian and undo that horrible paint job she has now. Laser scan the entire model for future use as well. ;)
Are there any motion control FX houses left in Hollywood these days?