Datum, the standard for aviation winds is 10m, winds are standard at this location for takeoff and braking performance. The winds are usually measured at only one location per airport. What can be worse if they are measured at multiple locations and then averaged together.
Cup anemometers only measure the horizontal component of the wind. When it is gusting, the cups tend to overspeed and keep running past the gust, hence the 10 minute average.
As you are alluding to, winds do not always blow completely horizontally, affected by structures and terrain. The Ekman spiral is typically used in aviation (procedure design) to estimate winds aloft and the direction rotation at altitude due to the influence of terrain drag and the Coriolis effect.
Wind seldom is completely horizontal, following a Kelvin Helmholtz type pattern
so it is important that the vertical wind component be measured due to uplift/downdraft components that are typical in winds.
