I don't see any problem with the experiment. You line up a row of shells, add the fish and observe what they do. You will get some result, even if it's "They don't care what sort of shell they live in", that's still a valid result.
Jazz it up with pictures of the fish and fry, and some fancy powerpoints and pie graphs, and you are all good.
The thing about School science experiments is not that you prove your theory correct, it's that you conduct the experiment in a scientific manner, and get some sort of result. Wether it fits the original theory or disproves it isn't the point, it's that you did the experiment and got some results.
Your plan is good, as either way, the fish will be OK, as opposed to those crap "bio-sphere" things they usually suggest. The Multies may live in the white shell, or the brown shell. They may breed, or not. But they shouldn't drop dead.
Carry On
Ian