Thank you, Daniel, for the feedback and the links. I have already been aware of the works of Charles Macal and the little book by Gaylord is nicely sitting on a shelf nearby.
My question is not as open-ended as it may seem: I did very precisely ask about the ability of Wolfram System Modeler to address agent-based models, e.g. where structure is created during run time and also terminated again. Also there is the ability to address multi-paradigm modeling (ABM, System Dynamics and Discrete Event Simulation) like AnyLogic further down the line of my question.
I am aware of the potential of Mathematica to address ABM especially when linked to other software like REPAST. But that is the point: Writing equations for larger models -- especially with structure that is repeatedly used -- is imho not really an option, so one needs some kind of declarative programming tool where graphical building blocks can be used (and reused).
So far it seems that modeling variable structure systems is not possible with WSM?