I rarely watch the Blu-Rays. Star Trek, or any show from that era, was never meant to be seen in Hi-Def. Many effects were made possible because of the limited broadcast resolution, providing them another layer to hide behind. Now, though, we can see threads hanging off uniforms, Spock's ear make up seams, Kirk's toupee line and other crap that pulls me out of the action.
No, I prefer the DVDs, but really mostly watch the laserdiscs. There everything is still hidden and you get the original sound mix to beet.
As for the quality of the effects, I grew up with them and they haven't changed. They're as good now as ever.