A battery looks like this:
simulate this circuit – Schematic created using CircuitLab
A battery is like an ideal voltage source. An ideal voltage source produces the same voltage no matter what. It doesn't matter if you sink 1 million Amps out of it, it will still give you the same voltage. If you put two ideal voltage sources in series, the voltages add. If you revers the polarity of one, it will fight the other one and the voltage will be subtracted.
A simmilar case applies to batteries. The ways that a battery is not like an ideal source is:
- It doesn't have unlimited current sourcing abilities
- The voltage drops the more current you pull from it (in the short term) it has series resistance
- The batterys voltage will drop the more energy you pull from it.
- It has internal resistance that is high (if you leave it there for a long time it will slowly degrade the battery.
So if you put two of the same batteries in series, it will double the voltage.
If you do this in the real world, it is important to match the batteries (which matches the series resistance, otherwise you can have more voltage running through one battery than the other and it will damage it or explode.
The middle doesn't 'short' because the voltage of the battery is pushing against the voltage of the other battery.