Anytime your private keys are stored on an internet connected device there always exists the possibility that the device is compromised and the private keys become known.
I am not sure what you mean by "linking" wallets.
Backups are great in case of loss or corruption but still do not prevent an attacker from stealing your keys. It is no different than having a backup of my ATM PIN. If someone has my card and pin then the backup is meaningless.
Encrypting your wallet is a bare minimum precaution you should be taking. I would not even consider using a wallet program that doesn't encrypt the private keys. Even then, appropriately coded software could be in place to extract the keys upon decryption or log the decryption string. Offline paper wallets are the only sure form of storage with regards to protection from theft.