Atahualpa is only slightly slower than the default theme (which has no options). You can easily verify this by switching back and forth between the default theme and Atahualpa. The hosting environment, the size of images, or the amount of plugins will have a much greater impact.
Don't get too worried about numbers such as DB queries or amount of calls to this or that function. While the raw numbers may indicate bad performance, in reality it boils down to a few microseconds. Add the time that WP itselfs consumes, plus the plugins, plus the momentary load on the web server, and any additional load caused by Atahualpa becomes quite marginal.
I am not denying that the code can be improved, and I will do that, however always do the real world test and see whether it is slow or not.