I remember reading that MM had a worse framerate than OoT, because Nintendo improved the textures / draw distance / area size / enemy count a lot, at the cost of a higher framerate. That's why I'm not sure if the VC version runs worse than the cartridge, cause MM was a low framerate game anyway, if I am correct.
The lag thing is a different issue though... I've noticed it with SMW and Zelda II, too, and on other TV's as well. It's really annoying, imo. I wonder why no one else ever complains about this.
Well Ocarina of Time ran at 20-25fps if I remember correctly so I highly doubt Majora's Mask had a lower framerate. Remember they used the expansion pack for that game which doubled the N64's RAM.
I really never noticed any lags but I should've noticed them in a fast-paced game like Starfox.