The proper way of doing things should be that an app controls access to jailbreak features. By default nothing gets them and you can whitelist the ones which need it. I'm not sure if anything like this exists for ios but it should.
Depending on how much access you have, it's always possible for jailbreaks to hide their presence from applications (which are running at a lower privilege level). There are a couple of "jailbreak hider" implementations out there.
