We study joint effect of specific features of the laser beam scanning and intensity fluctuations due to atmospheric turbulence on a signal recorded on horizontal paths with the visual laser navigation aids (LVNA). An experimental setup based on an ILD-2 laser dosimeter is considered as applied to measurement of the shape and duration of laser beacon signals. The estimated standard deviation of the intensity fluctuations at a receiver under different propagation conditions and for paths of up to ten kilometers long is compared with measured signal fluctuations being caused by scanning system. The range of signal variation under the joint effect of both factors is estimated, as well as the corresponding brightness fluctuations at visual observation. It is shown that the allowance for the joint effect of atmospheric turbulence and scanning is important both for obtaining quantitative data on fluctuations of the signal recorded and for developing engineering solutions to reduce this effect.