Well, the reason is really simple. The core "movie" sets all came out almost a month before the LOTR movie it was named after was released. This means they were developed while the editng and special effects for the movie were still in progress. This is why so many cards featured rare images from scenes deleted from the film.
Also remember that while the plot of movies was always known to any LOTR fan, some scenes and creatures were deliberately kept from public until release. I remember very fell pre-FOTR merchandising focusing on Cave Troll of Moria, but not showing the Balrog until very close to the premiere.
And of course some things couldn't be printed on cards because the visual effects for it weren't finished yet. Here are examples:
The Balrog, Twilight Nazgul, Watcher in the Water were not released until Mines of Moria.
Gollum, Treebeard, Ents and Wargs were not released until Battle of Helm's Deep (note that
Earthborn and
Oldest Living Thing cards from TTT use not the images from the movie, but promotional images).
Shelob and Army of the Dead were not released until Siege of Gondor.
So, basically the were two reason. One is that the special effects probably weren't finished at the time the set went to print. The second and more likely is: Decipher wasn't allowed to spoil major movie surprises.