With few exceptions, the labels putting out these complete scores on CD don't have the digital rights.
Also, for the GNP Crescendo expansions (Generations and First Contact), they are limited to 10,000 copies to save money on union reuse fees (at 10,000 units or lower, the AFM allows for a much cheaper, "archival" rate, making some of these titles financially feasible for the niche market who collects them).
I'm guessing the Trek II thru VI releases may be limited to 10,000 copies, but it isn't stated openly (perhaps studio wishes).
Either that, or the labels (FSM/Retrograde and Intrada) are hoping to keep the titles in print for a long enough time to make their money back.
Either way, unless Paramount wants to release the scores for digital download, it is unlikely we'll see them released that way.