A friend of mine is a mycologist who studies fungi that grow in hydroponic greenhouses. I feel fairly safe saying that there's no such thing as a "clean" environment where anything is allowed to grow. In the best case: if it's clean but nutritious enough to support life, it's ripe for rapid colonization, and probably by something nasty.

See also: biosphere experiments.

It is all good until it isn't and then it's massively expensive replacing or sterilising everything. I wonder how long realistically such level of cleanliness could on average be managed...

do you have any evidence of this? from my personal experience pests are an even bigger problem for growing plants indoors.

lack of predatory parts of the food chain allow some pests to go unchecked.

just one spider mite in a greenhouse... could quickly overtake the whole thing with out natural predators like lady bugs and predatory mites.

Just like fusion power.