If "ecosystem" (no hyphen) is defined as "a system formed by the interaction of a community of organisms within their environment," should "eco-system" (hyphenated) be used to describe a system formed by the interaction of a community of non-biological (say, electronic) elements within their environment? or does it matter?
Merriam-Webster defines ecosystem as:
ecosystem, noun : an ecological community considered together with the nonliving factors of its environment as a unit
However, ecosystem has been co-opted in the press in the past few years to describe, for example, the interrelationship between Apple's AppStore and its iDevices.
So, to answer the first part of your question, ecosystem has come to be used in the sense of the interaction of things (iPods, iPhones, iUsers) within their environment (iTunes, the AppStore), biological or not.
To answer the second part of your question, ecosystem is not hyphenated, and hyphenating it would not create a new word with a different meaning.
It would just be a system. The "eco" in "ecosystem" comes from ecology, which is a branch of biology, so it would not be appropriate to use it to describe non-biological systems (unless you are describing a system of artificially intelligent machines, and highlighting how life-like they are and how closely they resemble real, living beings).
From the freeonlinedictionary:
- A group of interacting, interrelated, or interdependent elements forming a complex whole.