Cryptic's missions reference the characters from the shows, albeit not going as far as to list their logs. I think that's pretty obviously OK since we get plenty of references there, but never actually see any of them. It's too bad, too. I wish they could get the rights to use some of them, or maybe even get some to be voice actors.
I know it's probably a bit more expensive than other options, but other companies were able to use their likenesses in previous ST games, so it's not unheard of. Getting Brett Spiner to play Data and fill us in on what's happened to him would add a lot to the game. Even getting some minor characters from the shows, like what was done with Leeta, would be nice. Anyway, I digress.