Does HOMER use any algorithm to compensate this variation per hour?

That's a good question.  No, HOMER does not attempt to account for variation of the wind with the time step.  It simply assumes a constant wind speed throughout the time step, which as you say slightly underestimates the power in the wind.  But this conservative assumption is undoubtedly outweighed by other optimistic assumptions, principally that the wind turbine will be available 100% of the time, and that it will perform as specified in the power curve.  If anything, we need to make HOMER's estimate of wind power production more conservative, not less.