His rhetorical questions prior to any real hominid finds do not accurately reflect the abundance of the fossils we have now, nor do they negate his theory.
His questions were more than rhetorical. Darwin's characterization of the fossil record was essentially a vast continuum of micro changes over vast periods of time. Not sudden jumps followed by long periods stasis as described by Gould and Eldredge.
Darwin and the fossil hunters who followed believed they would prove the "continuum". They failed.