I think they're supposed to make you feel more vulnerable by taking away your ability for combat. Encountering an enemy that you can't actually defeat should in theory make it a more tense and memorable experience. Unfortunately it tends to become a chore and a game or hide and seek. The thing is, it's a great mechanic to use when used sparingly. Amnesia was heavy on puzzle solving and exploring to create a tense atmosphere. The monsters appearance was something to actually fear because of how little it wasn't used; they're was a level of unknown. Your imagination will always create a scarier verison than the actual product.
The darkness and fear weren't really scary games to me, especially the darkness. Condemned did a better job of this because you were on the same level as the enemies (melee weapons, being outnumbered). Also something about melee combat creates a more intimate experience.