Recurrently coupled oscillators that are sufficiently heterogeneous and/or randomly coupled can show an asynchronous activity in which there are no significant correlations among the units of the network. The asynchronous state can nevertheless exhibit a rich temporal correlation statistics, that is generally difficult to capture theoretically. For randomly coupled rotator networks, it is possible to derive differential equations that determine the autocorrelation functions of the network noise and of the single elements in the network. So far, the theory has been restricted to statistically homogeneous networks, making it difficult to apply this framework to real-world networks, which are structured with respect to the properties of the single units and their connectivity. A particularly striking case are neural networks for which one has to distinguish between excitatory and inhibitory neurons, which drive their target neurons towards or away from firing threshold. To take into account network structures like that, here we extend the theory for rotator networks to the case of multiple populations. Specifically, we derive a system of differential equations that govern the self-consistent autocorrelation functions of the network fluctuations in the respective populations. We then apply this general theory to the special but important case of recurrent networks of excitatory and inhibitory units in the balanced case and compare our theory to numerical simulations. We inspect the effect of the network structure on the noise statistics by comparing our results to the case of an equivalent homogeneous network devoid of internal structure. Our results show that structured connectivity and heterogeneity of the oscillator type can both enhance or reduce the overall strength of the generated network noise and shape its temporal correlations.