Only seasons one and two need effects work. But to go HD they would need to redo it all.
Yeah, there's just no way around it, due to the nature of the film stock...
As for the FX aspect, I'd be happy if they just adopted the pragmatic conservativeness used in the TOS remaster... a mostly faithul re-rendering of the original shots, with the occasional flourish or enhancement where it would really make an impact, or when it can be used to cover plot holes, glitches or undo special FX failure from the original shots.
And having seen the job done with the TOS blu-ray, obviously it's possible to have your cake and eat it too, since they can keep the old shots for those that just want a cleaned up live-action picture.