Here is some info on turtles and salmonella.
Fish don't really carry salmonella but if you raise fish in water that is contaminated with salmonella then there could be salmonella on their skin. With cooking salmonella is not all that dangerous with the fish.
However, veggies in a system where you introduce animals known to regularly carry salmonella, I would just avoid it unless you tend to cook all veggies very well.
I have never heard of salmonella or e-coli getting from the roots up into fruit but I don't know the details of the salsa salmonella problem. I do know that lettuce can draw bacteria up into the plant so no amount of washing would protect you if eating raw salad greens from water heavily contaminated and since most people love fresh greens from their aquaponics, I would avoid the contamination.