From: Perth, Western Australia
I recall reading somewhere (I've just spent the past few minutes looking for a source and come up empty so take this with a big grain of salt) that just like the upper boundary of the layer reflects sonar pulses from ships on the surface, the upper and lower boundaries of the layer reflect sonar from submarines in the layer. This means that operating in the layer makes you tactically blind (unless you've got a towed array, but the vast majority of boats represented in the game don't).
I would imagine it's quite difficult to sink a ship you can't actually detect. Similarly, unless the opposition has a variable depth sonar (again, the vast majority of ships represented in the game don't), I imagine they'll have a rather difficult time detecting you. I'm not sure when it's a really great idea to be in a position where you definitely can't see the enemy and the enemy probably can't see you, but if they can - you're dead. Maybe it makes sense for boomers?
Since there seems to be limited tactical utility, it makes sense to me that the setting wouldn't be a default for the game. Why would you want the computer to be able to do as a default something that doesn't give it either an offensive or defensive advantage?
Addendum: See the CMO Manual pg 235-6 for further information about the implementation of "the layer" in-game.
Thanks Fido81. I' m aware that in the thermocline that you can be tactically blind. However, I imagine that there would be occasions, especially for SSBNs, to mask in the layer, say to and from launch zones...