I avoid the magnetic pistol even in the late war years, I find it unreliable I always go for impact shots. I like to go deep with my eels just to the point where the hull curvature starts to be pronounced. So depending on the ship's hull I act accordingly. If its a Large merchant for instance that if memory serves has keel below the waterline of 8.9 meters I shoot for 5.5m depth in calm seas and 4.5m in rough weather. There is nothing worst then seeing an eel set on impact sail right under the ship due to a heavy swell so make sure to allow for this worst case scenario. It is a large tanker that once again if memory serves has depth of 11.7 I shoot for 7.5 in calm seas and 6.5 in rough.
Like I said make sure not aim lower then where the curvature of the hull becomes pronounced i.e. for a large merchant do not shoot your eel at 7m depth. Odds are that the hull is to curved and the eel will bounce off without exploding.
I find that this maximizes the flooding, sinking ships faster and with less required hits.