It's not an intended realism/unrealism change or anything, it's a consequence of how permeable mesh logic works in the engine. If the launchers are below sea level it sees the water as a "wall" and thus missiles try to seek into the wall, but can't hit it since it's not solid so the missiles loop around constantly trying to hit it until they explode.
Anyone who was around in Beta or Reborn may remember similar things with bushes, except due to their awkward shape they'd make it hard to fire any weapon through them and not just tracking ones, plus surfacing fully is not quite as difficult as making sure that there's no bushes between you and your target.