In my copy of Peers' East Africa Foundry book he says the sources unfortunately do not describe the flags, but he goes on to speculate that they probably resembled East African Arab flags of the time, due to the massive cultural influence the Arabs had on the region at the time.
So that would probably be some variation of the Sultan of Zanzibar's flag, which was plain red. Strips of other coloured cloth would be added as differences, such as a wide white band at one end.
So I guess you can either get creative and design your own, or leave them out altogether if you don't want something you know to be false. Don't think the books are going to help us here.