If you don't understand why, check out the Babylon 5 DVDs. The effects there were rendered for 480p displays, while the non-effects shots look fine as they were filmed in a forward-looking format where they can easily be upconverted to HD. The result is everytime an effects shot is used (which is A LOT in B5), the video quality is highly pixelated. And that's just on standard resolution DVD; a HD release would look much worse.
I should point out that the visual effects on the Babylon 5 DVDs look so poor in SD because they have been blown up from a 4:3 source to fit a 16:9 frame. It is true that the effects without visual effects were shot with HD in mind, for they were filmed in Super 35mm and protected for a 16:9 frame.
This issue does not apply to any of the Star Trek series however, for every one except for Enterprise was shot on 35mm (like Babylon 5), but not protected for a 16:9 frame. The visual effects were still only mastered at 480p.
Model shots were photographed on 35mm film that could be recomposited for HD, but any CGI was only created at 480p and would have to be recreated. This is another issue where Babylon 5 runs afowl, but I suspect Trek won't (as badly, at least). Warner Bros. lost the original CGI models and shots used on Babylon 5. As far as I know, most of the CGI models used on Star Trek have been saved. These models may have to be upgraded to pass inspection in 1080p, but the extra step of re-creating them from scratch will not be required.
I am curious about those tests Paramount was running on upgrading Star Trek: The Next Generation's effects, though. Anyone have a link on that?