I've noticed this problem, too, but it seems to be sporadic. I remember it working on an attack against the HMS Hood while it was in port, but not against a Whaling ship. I remember it working against a large tanker, but not against some of the other ships.
However, the damage spots do show up on the Recognition manual, so all you really have to do is just aim the crosshairs of your scope where the damage spot is. I've been able to sink most ships pretty easily this way.
I think some of the bigger ships are more armored than they need to be, though. I mean, for a test, I saved a game when I had a perfect shot lined up on a BB. I tried different scenarios in regards to what methods of hitting the BB work best.
I found that one fish was not enough to seriously harm the ship, even when hit in the ammo bunker. Yet I found that even a second shot on the same location did nothing. Or a third.
I think, and I'm sure that the GWX devs would back me up on this, that it is better to sink the bigger ships through multiple holes. Though I do think that a hit on the ammo bunker might be able to do more damage (not critical, but why would two consecutive shots on an ammo bunker spark no fires or smoke?).
But in the end, if you really want to use the damage points, just try and "shoot from the hip" by aiming your scope in accordance with your recognition manual.
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