Why do you actually need to simulate them? The mapping between the state of the computer and the simulated state it represents exists only in our heads. You might as well say that any reality you can vaguely conceive of, exists and has moral weight.
Depending on which article you look at, you can see things such as the stunning, vivid rotating 3D model showing the optic lobes, or elaborations on what the model captures: it has mapped 139,000 neurons and 130 million synapses. I don't think that quietly picturing a fruit fly in your head executes a true simulation of those details.
I do think, in some cases, there is such a thing as thinking being equivalent to simulating (e.g. a calculator) but this isn't one of those.
