Yes you can set the spread angle, depth, etc for each individual torpedo. The auto-targetting (correct me if I'm wrong anyone) just handles range, AOB and speed. Everything else can be set by the Captain or kept at the default settings.
I too have hit mines before. It's usually a nasty surprise when I'm cruising along submerged with no contacts anywhere around and deep water beneath the keel.
As far as morale goes, I'd say that it would affect things like reload time, repair time and how quickly contacts are detected and identified. I'm not too sure about the specifics though and will defer to the experts among us!
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