@Christopher, are you sure Paramount still has the joint copyright license on books, etc.. I thought that had recently changed to all CBS. You would know better obviously since you deal with them more. I may be wrong.
Where Prime-universe content is concerned, CBS Studios has the sole copyright on tie-in material. But Abramsverse tie-ins (the comics, the young-adult novels, and the games) are copyrighted both by CBS and Paramount.
For instance, here's a shot of the copyright page to Countdown to Darkness #2
from IDW. You can see at the bottom (though it's hard to read) that it says,"(R) and (C) 2013 CBS Studios Inc. STAR TREK and related marks and trademarks [sic] of CBS Studios Inc. (C) 2013 Paramount Pictures Corporation. All Rights Reserved." (I think that middle part is supposed to say "...and related marks and logos are trademarks of...". That's what it says on the back of the first movie's novelization.)