To measure the density, a facet is required. Then, then through monitoring the number of hits per unit time per unit area, the pressure or density could be obtained. That's how molflow+ works, right?
However, when the beaming effect presents, e.g. a group of atoms with density n traveling forward sharing the same velocity vector, how could I know the density with a facet, that is parallel to the velocity vector, since they never hit the facet at all?
In the density calculation, both the number of hits and their orthogonal velocity component are monitored. That way the obtained density is independent of the facet orientation (you can check it by creating randomly oriented facets at the same point, they should display exactly the same density.
If a facet is parallel to the particles' direction, you'll still get some hits on it (since the source is usually not a point but a non-zero surface), but the deducted density will have high staistical scattering due to the low number of hits. So, to reply to your question, don't use parallel facets to sample a beam's density, transparent perpendicular facets will gather much more statistics.
One last hint is to use 2-sided facets. A one-sided facet would over- or underestimate the density depending if it's facing the beam or pointing away from it.