After much research and more than a little frustration, I have decided to fill these holes and eliminate them altogether.
These holes appear on U-995, very clearly, on the starboard side only. They do not exist on the port side.
I have had no luck finding a clear image of this area on a type VII. A few long distance shots of boats on their sides are too blurry to see clearly.
No schematics I have found show any intakes/discharges through the pressure hull to sea. They are always connected to one tank or another or go under the deck.
I feel I've been bitten by U-995 once again.