I've done a bit more testing in regards to the vertically offset hitboxes:
I haven't had it happen in custom battles yet. (Needs more testing)
It seems unaffected by weather, I've have had it happen around all times of day and weathers. (May need more testing)
It is reproducible with varying degrees of offset when repeatedly restarting an already generated campaign mission.
It happens to both manual and autogenerated designs.
It seems unrelated to old campaign save files. I've deleted my entire AppData/LocalLow/Game Labs folder and created a new campaign, but the bug reappeared.
It seems to affect predominantly small hulls for me, TBs, DDs, CLs, TRs. TBs and DDs seem affected most often though. (May vary for others)
It can affect ships of the same class in the same battle differently. Some will be fine, some offset to varying degrees up or down.
As for how it manifests:
The clickable box is offset from the visual model, it also often cannot be selected via click-drag box.
When sufficiently offset, the affected ship is immune to torpedoes. Torpedoes fired by the affected ship can hit non-offset ships just fine.
Should the offset be enough, the ship cannot ram or be rammed by any ship that isn't similarly offset.
All elements tied to the hitbox are offset, such as smoke, visual shellfire directed at the affected ship, and seemingly certain UI elements like structure/float bars, designation, name, and range indicators.