More than that, the idea that communicating via metaphor is necessarily dangerous and misleading seems wrong. These complex biological systems are indeed very different to our human experience. And in many cases our understanding is very nascent; requiring creative thought to develop new insights and make progress. In that context, using metaphors as hooks helps to guide our thoughts and suggest possible paths to further elucidation.
Of course, at some point one needs to back up the mental model with hypotheses that can be tested quantitatively, and to actually go out and do the experiment. And it is true that one can take the mental model implied by a metaphor and overapply it, making you believe you understand something that you don't. But that can also happen with any kind of model; one can learn some equations relating supply and demand and feel like that's sufficent to "understand eonomics" but end up making bad predictions when the real world situation turns out to more complex than the assumptions underlying the model.