The first time I played OoT, it was about 1 in the morning after I got the Lense of Truth, and was horrified. I had to go to bed and wait till the next day to get the nerve to go into the Shadow Temple. Now when I go through, it's still pretty freakin scary, and sometimes if it's night time when I'm playing I'll still wait till the day before going in. Not nearly as scary as the first time I went through though... that was crazy. I chose the second option.
I REALLY hope they have one spooky dungeon like this in SS... they don't need an entire game of trying to scare you, but one section of it just makes the game fun