Don't think U-Boats had thermometers but seem to remember that they could take water samples at various depths, and it was a particular crew member's duty to do this.
So its probably true to say that the existence of Thermoclines wouldn't be unknown to them.
If SHIV's implementation is only rudimentary, it sure beats not having it at all!! Seems that the SHIV engine has some pretty good things going for it. Was looking at Mikhayl's Type II conversion the other day. Must say it looked darned impressive.
Can't wait to see what the Atlantic campaign will be like when it gets ported over in its entirety.