I always thought the effects were done at 480p due to the render times?
I'm positive that at least a few shots over the years were done at 480p to save time, I recall someone on the show (Doug Drexler maybe?) mentioned this at the time and it was even discussed on this very BBS at one point. Unfortunately I can't find any reference to it now, I had started to think I imagined it but possibly not now.
EDIT: Found something, an article from early 2005
where Ronald B. Moore mentions that some shots were rendered in SD and then up-rezzed for time. There's also this thread
on another forum where someone mentions it, and also this post
on TrekBBS with some quotes from the above article and others, including one that implies that all VFX compositing was done in SD at one point.
Perhaps that's why some of the VFX shots look poor at 1080p?