yes, magnetic pistol can easily fail to explode if the torpedo runs at 90 degrees under a slender hull, which is why you will want to learn the various tactics at your disposal. magnetic is great when you are forced to shoot at, say, 30 degrees AOB. because the torpedo will spend a lot more time underneath the hull.
'critical' points besides the already mentioned engine room are: masts (specially forward) and guns. i sometimes get the huge secondary explosions and sinking because i got a torpedo in the ammo bunker for some gun (once took out an auxiliary cruiser with one impact shot right under her fore gun platforms. it made my graphics card go all laggy
WO assistance is a good way to upgrade your realism, you can start doing the calculations and 'check' them against your officer's solution
good luck