I've never seen any fx guy or production person address this before. What makes you think that we were supposed to see thruster action besides a script reference?
The script calls for "thruster jets firing" after Kirk's "thrusters at stationkeeping" order, but IIRC the effect that ILM came up with looked too much like the normal flashing of running lights (just a blinking yellow thing) and was therefore dropped. You see a smaller scale example of this in the deleted scene where Kirk leaves the Enterprise in his space suit; the corners of his thrusters flash yellow along with the hissing sound effect, consistent with script cues.
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I remember little animation flashes when you first see the guy outside epsilon 9 during a cutaway from the klingon battle, but I don't remember the bit you mention, is it just a practical light?
Again, I've read just about everything on TMP (and interviewed several of the vfx guys) and have never seen anything at all about ship thruster animation even being attempted. And Trumbull had some of the best guys for this (Bob Swarthe, for one), so they could have done something marvelous if they were so inclined, a lot better than anything ILM could have done on the followups even if they subcontracted to VCE like they did for most of the TWOK animation.
It was an old magazine published almost twenty years ago, so I don't know if I can still find it (have ALOT of that junk lying around in my basement). It was a producer decision, not a VFX one; the thruster animations were indeed added at appropriate times for the little guys in the space suits and even the Vulcan warp sled, but there was some concern whether people would mistake them for running lights or strobes of some sort (as many people did for the Vulcan ship) so they were left out of the final cuts.
It's one of the things they just didn't have time to figure out on the movie's production schedule, so they didn't bother. Sort of like the whole "memory wall" fiasco, they threw together a makeshift solution that was, in the end, entirely satisfactory.