Magnetic influence isn't a 'triggered' detonation, it refers to the payload using a magnetically-influenced trigger that would activate upon passing under the target within (usually) 2 meters. First and foremost, I have no idea how the schematics work out, so I could be off by a mile on the exact 'how,' but the likely scenarios are that the detonator itself has a magnet attracted to the hull of the above ship, or that for reasons unknown to me, ships exert their own electromagnetic field that the torpedo responds to.
Regardless of the technicalities, the point is that enabling the mags will cause a nice, pretty, and usually much more effective BOOM when passing just under the target's keel; as far as SH4 is concerned, there's no reason not to enable it. If you get a dead-on hit, you'll happily take a contact detonation, or if they run deep, there's nothing wrong with a keel shot either.

Check out a very useful resource I found on the "Official" (Hah!) forums
here for some more torpedo data.
The reason that keel shots are more effective is still a bit beyond me... I might have to offer my own minor thread hijack, in fact! I've always worked under the assumption that most seafaring vessels have a V-shaped hull, but isn't it the nature of a V-shaped body to offer more deflection than absorption?