Y'know, maybe JMS is like me and decided that having a technomage running around helping Sheridan really undermined the power of that episode, and so has decided to overlook it.
Perhaps JMS just didn't want to
spoil the novels for people who have not read them yet. IMHO, the power of the episode was
not undermined by what happened on Z'ha'dum in the Technomage novels.
After all, the defensive system is never really alluded to in the show itself, and it could easily be argued that the majority of the available Shadow ships were off at B5, so why bother explaining a problem that the novels made up?
It's not a problem. It wouldn't have mattered if 1000 Shadow Battlecrabs would have been at Z'ha'dum when the Whitestar was crashed into the planet. All the battlecrabs were under the control of The Eye.
There's no visual obstacle to the White Star in the episode itself, and so down it goes without trouble.
You're right in that we see no battlecrabs at Z'ha'dum when Sheridan caused the Whitestar to crash into that planet. However, because we don't see/hear Galen on Z'ha'dum in the episode, it doesn't mean that Galen wasn't there. In almost all cases, Cavelos has deftly woven the Technomage trilogy into the episodes that the trilogy touched (e.g. The Geometry of Shadows, Interludes and Examinations, Z'ha'dum, and Epiphanies).
IMHO, The Technomage trilogy gets rid of this problem:
Lurker's Guide "Z'ha'dum" Analysis
"Z'ha'dum's defenses are similarly flawed; the White Star was able to crash into the surface of the planet intact, apparently with no opposition on the way down. Why weren't the Shadows vigorously protecting their homeworld? Obviously they left the White Star alone while it was in orbit because of their guarantee to Sheridan, but once it started plummeting toward one of their cities, it's odd that they didn't shoot it out of the sky."
There are only a couple of places where Cavelos blundered, and this is not one of them.