I never really found anything in the Legend of Zelda series to be frightening. Creepy when thought about, sure, but nothing scary. I found ReDeads more annoying then terrifying. Maybe if the Legend of Zelda looked more realistic and graphic then maybe some enemies would look scary if they went the dark and gritty route.
I think the N64 graphics pulled that off quite well. For some reason, I don't see this happening in OoT3D. The colors and textures would seem too vibrant and clear in comparison to the gritty texture of the N64's graphics. That gritty faded texture helped boost the scare factor of the Shadow Temple up a bit. That's just me though, I guess.