The new digital pins 20-35 can only be used for output, not input. They cannot source or sink as much current as normal Arduino pins. An Arduino pin can source/sink 40mA, but the outputs the EZ-Expander shield can only source/sink 6mA. This is still enough to light an LED with an appropriately sized resistor to limit the current (e.g. 470 ohms), and, of course, you can use transistors to drive higher loads. See the 74HC595
datasheet for specifications.
All other Arduino pins are brought up to the top of the shield for easy access. Since pins 8 (latch), 12 (clock), and 13 (data) are used by the shield, they are not available for use and are marked with an 'X' on the silkscreen. Pins 8, 12, and 13 are chosen to control the shield as to not use up any PWM-capable pins (9, 10, 11).