I can tell you about those "invisible enemies". They are an illusion of sorts but a deadly one as you found out. In fact I have a thread about it.
When you use a mod that alters the game's enemy aircraft to become less frequent but more effective a strange thing then happens.
If you dive after the crew spots one but do not go deep enough and go back into time accelration mode ....the planes "nail" you.
However:
For some reason the damage doesn't register until you come out of time acceleration....then it hits home with vehemence.
Naturally the plane is long gone..you thought you had escaped detection and destruction by it...and once the damage registers you are left with a feeling of having been done in by some invisible enemy....
There are two cures that I know of:
1. Never dive when you spot a plane to just periscope depth. Crash dive and go way down fast... at least to 140 feet.
2. Install Webster's fewer planes mod. It reduces the number of enemy AC out of range of land bases but doesn't give the planes "super" detection and/or destructive powers.
I choose option 2 and after several patrols have not had the problem of being hit by AC after submerging reoccur.