I guess it's a similar concept to topping up your engine oil, sure it will be below the minimum mark on the dipstick, but the car still runs fine, although it's not a good idea, as it may affect the efficiency of the engine, if the air conditioner hasn't got the right amount of refridgerant, then surely there must be something else in there instead, (air?) the compressor will try to compress air and there will be air floating around the system surely? That should therefore mean the compressor is working harder?
The space will be occupied by vapour basicaly, as the the refrigerant leaks out out, less liquid is produced and you end up with flash gas (liquid vapour mix) going to the evaporator which means amount of heat being removed from the medium is reduced.
Only time air gets into the system if the charge has completely escaped or the low side has a leak the charge is low and a vacuum is formed then the air will get sucked in.
Lower the charge less stress on the engine as there is more space in the condenser to condense the vapour which means lower head pressures and less stress on the engine!
Rob