Because the pendulum drives the clock and the shorter it is the less far it has to travel and so it runs faster.
To demonstrate, If you take a length of string and put a heavy weight on the end and then swing it back and forth the shorter the string the faster it goes.
The time period of the pendulum increases as the length of the pendulum increases, therefore your clock would run slower (and vice-versa). Clock pendula are "compensated" so their length reamins constant as the temperature changes.