To recap: the short circuit current is a function of several variables but is mostly determined by the nominal voltage and internal series resistance. If the positive and negative terminals are connected by a wire then the battery is by definition shorted. What the voltage of the battery is does not really matter.
the battery emf causes the current, not the terminal voltage. If you short-circuit the battery, the emf drives a large current through the internal resistance and the short-circuit, but the terminal voltage is zero.
Now remember, that a model for a battery is an ideal voltage source, internal resistance. when you start pulling current from the battery and complete the load there will be a voltage drop rI corresponding to the voltage drop due to the internal resistance this will cause the voltage of the cell to be lower than the voltage of the voltage source.
This usually happens during some-or-other incident, but it can also be the result of human carelessness or malice. Short circuiting a battery deliberately, or accidentally connects the positive and negative battery nodes, forcing them to be the same voltage. The result, as Wikipedia puts it aptly, is a connection with almost no resistance.
A short circuit in a battery is the formation of a low resistance path between the terminals. This results in the battery's internal resistance dominating the circuit's overall resistance.
Eventually, with a shorted out battery the current taken is at maximum but the terminal voltage is zero. The internal resistance of the cell causes this to happen. If a cell didn't have internal resistance it could supply any amount of current without the terminal voltage falling (an impossibility of course).