Another option you can do is use epoxy caps.
We use them in the Navy to prevent tampering on sensitive engineering equipment.
Very easy to install, a bitch to remove.
All you need is a tube/pipe with a diameter slightly larger than the bolt or nut's head you are looking to protect. Place the tube over it, pour in the epoxy so that the head of the bolt/nut is completely covered allow the export to cure then remove the tube or cut it off just above the epoxy. Cardboard tubes work best so that you can peel them off afterward. I would recommend pre-cutting metal tubes/pipes if you want to use them for the mold.
Depending on the epoxy you choose, it may only be removed with a chisel or an angle grinder.