While watching a third season ep tonight on normal DVD, I noticed the nacelles spikes somewhat visible on a flyby during the opening.
If the spikes were only partially visible, it’s because the stock flyby shots from the pilots were constantly re-used in new production episodes, with increasing image degradation each time the footage was printed another generation. Roto-matting the spikes out would have been a waste of time and money.
If I may add a tad...
From my studies of the film, there are several major reasons why the effects shots using models were degraded:
1. Film Stock: Interpositive and internegative film copies were struck from the original camera negatives so that the OCNs could be safely stored away. As far as I can tell, most of the effects shots were done off of these intermediates (usually the interpositive). And, although they used fine grained and low contrast film to make these copies, contrast and grain build-up resulted in a reduction of quality in the final print, even in the absence of any optical printing (see #2 below). I have many of these interpositives in my collection, and they are dark and surprisingly grainy relative to the OCN.
2. Optical Printing: When the various optical elements (e.g., film of the model, film of the planet, film with the male and/or female mattes, etc.) were composited (printed together) in the printer, the final print was degraded due to slight focus issues, slight registration errors, hair and dust, fingerprints, contrast and grain build-up from multiple passes, etc.
3. Mattes: The male and female mattes they generated to isolate the foreground and background elements for the compositing were often the result of a color-separation step-printing process onto high-contrast black and white film. Generally, their quality varied considerably from shot-to-shot for reasons similar as discussed above. This was not a perfect process and did not always isolate the elements correctly. When parts of the Enterprise unintentionally appear to wink-out or vanish, it was usually a failure of the matte.
But you know, all things considered, I think it's amazing that the effects shots worked as well as they did!
Oops, sorry, maybe that was a little more than a tad...