If there were no air resistance, the final speed when the ball was caught would be the same as the initial speed. This is a consequence of the conservation of energy. The initial and final kinetic energies would be the same because there is no change in potential energy.
However, when there is air resistance, mechanical energy is not conserved. Some energy from the mechanical system gets converted to heat. Since energy is lost to the mechanical system (that is the kinetic energy of the ball and the gravitational potential energy), the final kinetic energy must be less than the initial kinetic energy. Since kinetic energy is proportional to speed squared, the the final speed (the speed when caught) will be less than the initial speed.