Why a stratus cloud does not always reach all the way to the ground?
I'd postulate that this is purely temperature-driven. 

If the dew point temperature of your 'empty' layer is not reached then the water vapour will not condense to form fog. 

Do you observe the clouds there during the day? Thin clouds such as stratus primarily transmit incoming solar radiation whilst trapping some of the outgoing long-wave radiation, thus insulating the air between the ground and the base of the cloud layer and preventing dew point temperature being reached.