Lightfeathers,
The fish do occasionally pass through the coral. I see it most often on the left coral 'tower'. I can't really see a fish passing thru on your 2nd picture but I have seen fish passing thru coral quite a few times so I believe you.
I'm crossing my fingers that Jim will track down some awesome collision detection code and use it in conjunction with his 3D coral background he's working on.
And he IS working on it. There's rumors of clams.
And no, they won't be ready for a while so don't ask.