I think any skulls cat/racoon sized would last a while, possibly years, depending on what chews on them. When I've found them in streams, they have been pretty thoroughly covered with moss/algae. I imagine it will get covered with algae pretty quickly in the aquarium, but maybe not.
Smaller, like rabbit/ squirrell and stuff would probably get chewed up/fall apart a lot quicker.
I've coated/filled skulls with epoxy resin before (but not used in aquariums). It's better if you have a mix with a long cure time, so that it can soak into the bone.
I don't know about silicone, I think it would start to fray and peel off in sheets after a while.
If you put a turtle shell in, I think it would be a really good idea to coat it with resin - they tend to fall apart after a little while