Please advise on input for altitude. Does this value needs to be equivalent to the hub height? Or should it defaulted to zero?

HOMER uses the altitude of your site to determine the density of the air and the energy that the air's movement contains.  Air is denser at sea level than it is at a higher altitude and will therefore carry and transfer more energy to the blades of a wind turbine than air moving at the same speed at a higher altitude. 

For this parameter, simply input the altitude of the site where you turbine will be installed.

Any difference between hub height and anemometer height will be used to calculate the difference in wind speed between these two heights.