If you want to know where a ship's torpedo-protection is, look at the armour profile and the bulging parts midships (which would be the torpedo bulge). The torpedo-protection doesn't go around the whole ship but is concentrated midships. If you have a ship with good torpedo-protection, there's where you'd like the torpedo to hit.
On ships with poor torpedo-protection (or none at all) you want to exploit the damage saturation mechanic and take it on the bow or aft ends (as those sections saturate quickly). You're almost guaranteed to get a flooding if you catch a bow on those extremeties though, so keep that in mind.