Do you have koi alone or with other fish? I have koi in my systems and in a koi pond. The koi in the aquaponic systems, with lots of tilapia, act like the tilapia. They act scared and hide on the bottom with the school most of the time. My koi in the pond, on the other hand, are only with other koi. They are friendly and will actually beg for food. My pond fish are much more pleasing to keep than tilapia. Since I discovered this difference in interaction I have changed my philosophy on the best fish for systems.
New fish in a system need time to get used to you and the routine. The less you net and mess with them in their environment, the more friendly they will get. Follow Chi's advice and you should see your fish more