How well are neurotransmitters used in SPA?
At this point in time, the difference in neurotransmitter types affect the synaptic time constant (i.e. the filter on the incoming spike train) between neurons in Nengo. See Neural Engineering p.112 and these notes (see the section called "Biologically plausible filter") from a course covering the book.

Neurotransmitters are also leveraged more theoretically. For example, in connection between neurons that involve learning, dopamine is often said to modulate this learning. For example, see Dan Rasmussen's neural hierarchical reinfrocement learning implementation (PHD link pending).

Hypothetically, it would be possible to implement a back-end to Nengo using a more biologically detailed software such as Neuron to take into account neurotransmitter generation, concentration and consumption. Although I can attest anecdotally that this has been attempted with mixed success, there has been no formal release or publication of this approach.