Empty airplanes can happen at the major level, too. Usually this is because a flight was extremely delayed due to mechanical concerns or sometimes weather issues. Typically the airlines will not cancel a flight just because the passenger count is low. While that one flight might not have a lot of people, the next flight in the aircraft routing might be full, or the airplane is simply needed somewhere down the road to make up another flight. In addition to this, it just isn’t a good look to cancel a flight just because the load is low on it, that is a very quick way to make disgruntled passengers.
As far as the pilots are concerned, it really doesn’t matter to us if the flight is completely full or completely empty, once that cockpit door closes, we conduct ourselves in the same manner no matter what. The airplanes obviously weigh less when they are empty and sometimes have a tendency to want to leap off the ground on takeoff or float on landing. Pilots of course anticipate this and respond accordingly.