Are Star Trek novels allowed to cross over with other franchises
As mentioned, "Ishmael" crosses over with "Here Come the Brides". As that TV show was a Paramount venture, the Pocket editor of the day didn't panic too much when she realised it was an unofficial crossover, then discovered the rights had passed to a new owner and Pocket had to scramble to clear it.
There are humorous cameos as well: characters from "Bonanza", "Have Gun, Will Travel", "Maverick", "Doctor Who" and "Battlestar Galactica".
The use of Larry Niven's kzinti (from his "Known Space" books and the "Ringworld" series) in Filmation's TAS has meant the kzinti also made a cameo in Diane Carey's "Battlestations!" They were intended to play a major role in "The Captains' Honor", but were changed to the felinoid M'dok at the last minute.
Incidentally, the character Picard faces off against in "The Captain's Honor", Lucius Aelius Sejanus
of Magna Roma (the "Bread and Circuses" planet), is supposedly inspired by Patrick Stewart's Sejanus in "I, Claudius".