Licensing is the issue. Since IDW holds the comic licenses for both Star Trek and Doctor Who, they can do that crossover. Likewise, Marvel held the Trek comic license and Pocket Books held the novel licenses for both Trek and Marvel back in the 90s which is how we got the Trek/X-Men crossover.
There definately won't a Trek/Doctor Who novel crossover since Pocket doesn't have the Who license (Who novels are published by the BBC themselves).
We can also rule out crossovers of any other kind, unless its with a franchise that Pocket or IDW also have the license for. Which means no Star Trek/Stargate crossover and certainly no Star Trek/Star Wars crossover.