You seem to have a slight misunderstanding of how crypto wallets in general work. They don't "store" coins, they store private keys that allow you to transfer the value you own on the blockchain, which is public and distributed. The coins are never in your wallet, they are never in any one place. They exist due to the consensus of the network.
Bitshares is no different, the wallet stores your keys. The keys allow you to transfer the value of your BTS or other assets.
Whether or not a particular asset on the bitshares network is more free of counter party risk will depend on the asset, but in general BTS and the bitX smartcoins carry no counter party risk and therefore less risk than anything you have on a centralized exchange.