This is like that stupid embargo thing WB did when they wouldn't let people making the cartoon "The Batman" use The Scarecrow and Ra's Al Ghul because they were being used in "Batman Begins" and then "Justice League" couldn't use The Riddler because he was on "The Batman".
It's idiotic and makes no sense. Supposedly the reason is because viewers would get "confused" seeing all these different interpretations of the same character out there in pop culture at the same time. Yeah, right. This is the same kind of thinking Paramount probably had.
Like the universe is going to collapse on itself if the Enterprise-E is shown on screen in "Star Trek: Deep Space Nine" while the TNG movie series is still active. A tiny little cameo just to add some weight to the war by showing that the flagship is involved wouldn't hurt anyone. I would have liked to see cameos from the whole cast of that series too, but I know that would be harder to do for budget reasons, so I don't mind it not happening so much. On the other hand, I don't think there's any good reason for the Enterprise not being in at least one shot.