The full time for the full layer is calculated, if this is shorter then the minimal layer time, the speed is slowed down so the layer meets the minimal layer time. But, it's never slowed down more then the minimal speed. (which you generally not hit unless you have a few mm2 of area). If this happens, the "cool lift head" feature can trigger if this is enabled, which lifts the head to make up for the time not reached by the minimal layer time.
https://github.com/Ultimaker/CuraEngine/blob/master/src/gcodeExport.cpp#L543