1. There used to be a Matlab toolbox for WSNs. So you can use it.
2. In Matlab scripts every entry is a matrix. So you may code, and represent connection s with matrices.
3. Ideally, you may want to learn the generally accepted WSN simulators for research: NS2, NS3, Omnet, Opnet. In the NS you may find a steep learning curve.
There are many ways to actually model a WSN in general. One interesting way of doing it is by modelling the interaction among sensor nodes (SNs) using graph theory. It enables you to further do signal processing on graph and so on. Have a look at our papers below to put it in context and clarify your mind before you decide on what tools to use and what modelling:
Article Distributed Two-Step Quantized Fusion Rules via Consensus Al...