I've never encoutered mines either in the game but i have not gone into harbours as that was next to never done and i like to just head out to the convoy lanes.
The channel was off limits to u-boats because of them pretty early on and there were a lot of mines drop into the north sea and Bay of Biscay to try and neutrilize shipping.
I expect an encounter would however go something like this...
sailing along-
run over magnetic fused mine lying sedately on the sea floor (you would never see especially through your scope), followed by catastrophic structural failure leading to all hands lost at sea.
probably with no message sent to BdU as to where or what happened to you.
Having mines in game to my mind should be there as they were no go zones (area denial i think is what they call it) but next to those acoustic torpedoes which were almost in game just would'nt be much fun for all those hours spent on your campaign.