Different level of analysis. The behaviour of a whole network depends not only on the chemistry of synapses, transmitter, second messengers, gene expression, and so on, it also depends on how neurons are connected. Connectomics is about two levels up from synapses. It looks not so much at the details fo the local connections, more at how strongly different bits of the brain are connected, because that is all that structural MRI can do. It doesn't have the resolution for tracking the details of small circuits.
Connectomics tells you something that perfect knowledge of neurochemistry wouldn't, and there are methods for studying it, so why wait?