My theory is, although Shedinja is a bug type Pokemon, it is still just the old shed skin of Nincada, not really even alive as its pokedex entry states:
SHEDINJA’s hard body doesn’t move - not even a twitch. In fact, its body appears to be merely a hollow shell. It is believed that this POKéMON will steal the spirit of anyone peering into its hollow body from its back.
So yeah, although it is alive in some sense, a discarded bug shell is made of natural substances and minerals.
That's just my theory. In the end only Gamefreak can really tell you.