I don't know what's going to happen as my colony grows out. I'll have to deal with that when I come to it.
I'm not sure what you mean by putting silicone in the shells. You mean trying to seal up the tip with silicone sealant? It sounds like a mess, and I'm not sure how well it would work. They make expanding foam... I think it has a flexible nozzle, and they make it for ponds, so it's tank safe. You might be able to push that in there and a little blob would expand to block the end.
I've read posts about fish being stuck in shells, but my multis haven't had a problem with these. I've only had mine for a month, but I have removed shells from the tank with the fish still in them (which you'd think would cause the fish to get as deep in the shell as was fishly possible), then put the shells back in the tank, and nobody got stuck.
Just so you know, I wasn't trying to torture my fish.

I just couldn't tell which shells had fish and which didn't. When I cleared an area I knew was someone's territory, I figured I must have removed him, and then put all the shells back in.