I don't mean to highjack this thread, but I've been itching for a long time to find a place to comment on this topic.
When I was a kid in the '70's, I remember seeing the "different" images of the TOS Enterprise. I assumed that the nacelles had different modes, which cause parts of them to shift or retract, thus changing the appearance. (This never explained the change in the color of the front-end of the nacelles, though.)
As I came to accept that we were actually seeing two or three different versions of the Enterprise model, each representing a different era, I accept this as another subtle form of discontinuity (the limited production values of 1960's TV FX).
More recently, a different view, somewhat revisionist, came to mind. Maybe the read spheres were there all along, but the "cheese grater" structure was added to cover over top of the spheres. I assumed that the "cheese grater" acted as a filter or stabilizer for the warp engines; these were likely used in the early days of the Constitution-class starships as an improvised refinement. By the TOS years, warp engines had been refit with built-in refinements that allowed the ship to run faster and more smoothly. With the built-in refinements, the "cheese grater" filtering technology was no longer necessary. These appliques were removed, and the refit nacelles were somewhat shorter. (I know they don't look that way, but I assumed that either the overall length would go down or the removal of the filters would allow the refit engines to stick out the back more.)