At my school there is a greenhouse, and over the past 7 years my school has taught with aquaponics in the greenhouse. There are going to be many small aquaponics systems: has anyone had problems with separate ecosystems in a contained room, where there can be outbreaks of pests? Has anyone had successes with multiple systems? If I'm missing any information about the question please tell me; I'll try to gather the information soon.
Eric - more the better in educational situations. You learn something different with each set up. As for pest management it will not make a difference. If you have them, you will have the problem through out the whole greenhouse, so the fact you have different systems will not make a difference. I have been a commercial grower running 10's of thousands of sq feet growing area and once hit everything will be effected so you just manage it. Works the same way in small greenhouse environments.
We have two systems, one running floating and shelves, the other running a larger bed and two verticles. As Rik said, when pests hit, they hit it all, even the garden outside of the greenhouse. The systems might be divided, but the pests are united!