I think your like me and may be overthinking this one. I'm no expert but I think not. IMO if your fishing a Zara spook then yes they will only hit them so many times before the figure out its not food. That Beeing said you can still get reaction strike when you catch them off Gaurd. But a live bluegill I think not. If there forage is bluegill and they don't eat it they die. How many bluegill do they eat for the one you catch it on? If say more than you realize. I'd say no matter how many times you catch him if his food is bluegill and you can present it as a natural bluegill he will bite. An overfished pond you will catch less, an under fished pond you will catch more. Do you want to catch a lot a couple times a year or a few whenever you want?
In rereadiin your post I see I didn't come close to answering your questions. I would say yes you would condition them less to a bluegill if you used shiners, would it be worth the effort, that would be up to you.