When the inputs to the PLC are scanned the physical input values are copied into memory. When the outputs to a PLC are scanned they are copied from memory to the physical outputs. When the ladder logic is scanned it uses the values in memory, not the actual input or output values.
The primary reason for doing this is so that if a program uses an input value in multiple places, a change in the input value will not invalidate the logic. Also, if output bits were changed as each bit was changed, instead of all at once at the end of the scan the PLC would operate much slower